rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
23,DRR334968,DRX323964,DRS217304,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 28 degrees rep 3,SAMD00422588,,sample name:mRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422588,DRX323964,m28 3 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422588,,,,3157078356.0,31416275.0,DRR334968,0:100.49 1:0,A:816263259;C:752748024;G:759884392;T:828182261;N:420,100,0,,,816263259,752748024,759884392,828182261,420,DRX323964,DRS217304,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.64888,,0.01832,,0.73996,,0.46811,,99,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
24,DRR334967,DRX323963,DRS217303,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 28 degrees rep 2,SAMD00422587,,sample name:mRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422587,DRX323963,m28 2 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422587,,,,3155807651.0,31404635.0,DRR334967,0:100.49 1:0,A:819014350;C:749873295;G:756284406;T:830635394;N:206,100,0,,,819014350,749873295,756284406,830635394,206,DRX323963,DRS217303,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.76742,,0.02238,,0.72427,,0.47376,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
25,DRR334966,DRX323962,DRS217302,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 28 degrees rep 1,SAMD00422586,,sample name:mRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422586,DRX323962,m28 1 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422586,,,,2589772286.0,25765782.0,DRR334966,0:100.51 1:0,A:679223577;C:610675892;G:617869465;T:682003195;N:157,100,0,,,679223577,610675892,617869465,682003195,157,DRX323962,DRS217302,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.42984,,0.03367,,0.73555,,0.49223,,100,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
26,DRR334965,DRX323961,DRS217318,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 19 degrees rep 3,SAMD00422602,,sample name:mRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422602,DRX323961,m19 3 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422602,,,,3124746628.0,31095367.0,DRR334965,0:100.49 1:0,A:821891547;C:734660854;G:739230475;T:828963220;N:532,100,0,,,821891547,734660854,739230475,828963220,532,DRX323961,DRS217318,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.72881,,0.03264,,0.69449,,0.47416,,99,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
27,DRR334964,DRX323960,DRS217317,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 19 degrees rep 2,SAMD00422601,,sample name:mRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422601,DRX323960,m19 2 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422601,,,,3171661466.0,31561473.0,DRR334964,0:100.49 1:0,A:836793307;C:742872021;G:750053514;T:841942389;N:235,100,0,,,836793307,742872021,750053514,841942389,235,DRX323960,DRS217317,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.63153,,0.03639,,0.69027,,0.48494,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
28,DRR334963,DRX323959,DRS217316,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 19 degrees rep 1,SAMD00422600,,sample name:mRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422600,DRX323959,m19 1 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422600,,,,2916453082.0,29023768.0,DRR334963,0:100.48 1:0,A:761416880;C:692014182;G:696272089;T:766749729;N:202,100,0,,,761416880,692014182,696272089,766749729,202,DRX323959,DRS217316,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.71651,,0.03406,,0.68696,,0.47496,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
29,DRR334962,DRX323958,DRS217315,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 10 degrees rep 3,SAMD00422599,,sample name:mRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422599,DRX323958,m10 3 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422599,,,,2600103192.0,25872833.0,DRR334962,0:100.50 1:0,A:668944597;C:625686885;G:631010166;T:674461210;N:334,100,0,,,668944597,625686885,631010166,674461210,334,DRX323958,DRS217315,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.57077,,0.02949,,0.71918,,0.47633,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
30,DRR334961,DRX323957,DRS217314,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 10 degrees rep 2,SAMD00422598,,sample name:mRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422598,DRX323957,m10 2 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422598,,,,2608660833.0,25958804.0,DRR334961,0:100.49 1:0,A:683370128;C:615324906;G:621209484;T:688756167;N:148,100,0,,,683370128,615324906,621209484,688756167,148,DRX323957,DRS217314,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.63764,,0.04316,,0.69656,,0.48579,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
31,DRR334960,DRX323956,DRS217301,DRP008001,PRJDB12578,Allometric scaling of RNA abundance from genes to communities,DRP008001,Other,The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole  body RNA content in organisms. However  testing RNA allometric scaling with next generation sequencing is yet to be done. Here  we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling  while the assumed temperature dependence appeared to be weak. Lastly  allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.,,,mRNA metatranscriptomic sequences from mock communities consist of five model species,mRNA mock community at 10 degrees rep 1,SAMD00422585,,sample name:mRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:mRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422585,DRX323956,m10 1 mRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008001,NextSeq 2000 sequencing of SAMD00422585,,,,2879915507.0,28651533.0,DRR334960,0:100.52 1:0,A:761972464;C:675761096;G:678969165;T:763212637;N:145,100,0,,,761972464,675761096,678969165,763212637,145,DRX323956,DRS217301,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.47851,,0.05671,,0.72622,,0.49269,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
101,DRR189403,DRX179868,DRS200418,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 3,SAMD00182246,,sample name:CSUS Tel 30 2w memory 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182246,DRX179868,CSUS Tel 30 2w memory 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182246,,,,2791119960.0,77531110.0,DRR189403,0:36,A:685050951;C:641519684;G:664655385;T:799677669;N:216271,36,,,,685050951,641519684,664655385,799677669,216271,DRX179868,DRS200418,DRA008865,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89653,,0.1773,,0.70725,,0.49873,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Brain,Nervous System
102,DRR189402,DRX179867,DRS200417,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 2,SAMD00182245,,sample name:CSUS Tel 30 2w memory 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182245,DRX179867,CSUS Tel 30 2w memory 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182245,,,,1505449224.0,41818034.0,DRR189402,0:36,A:369895057;C:346914787;G:358624651;T:429897489;N:117240,36,,,,369895057,346914787,358624651,429897489,117240,DRX179867,DRS200417,DRA008865,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89514,,0.17677,,0.7025,,0.49571,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Brain,Nervous System
103,DRR189401,DRX179866,DRS200416,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 2 weeks memory test in non trace 2 Way Active Avoidance coditioning 1,SAMD00182244,,sample name:CSUS Tel 30 2w memory 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182244,DRX179866,CSUS Tel 30 2w memory 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182244,,,,2088507024.0,58014084.0,DRR189401,0:36,A:516255405;C:478036869;G:496415722;T:597637091;N:161937,36,,,,516255405,478036869,496415722,597637091,161937,DRX179866,DRS200416,DRA008865,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89533,,0.18553,,0.70981,,0.49554,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Brain,Nervous System
104,DRR189400,DRX179865,DRS200401,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 3,SAMD00182243,,sample name:CSUS Tel 30 1d memory 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182243,DRX179865,CSUS Tel 30 1d memory 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182243,,,,1340808120.0,37244670.0,DRR189400,0:36,A:330513975;C:306935584;G:320089399;T:383165274;N:103888,36,,,,330513975,306935584,320089399,383165274,103888,DRX179865,DRS200401,DRA008864,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89272,,0.19494,,0.70335,,0.49456,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
105,DRR189399,DRX179864,DRS200400,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 2,SAMD00182242,,sample name:CSUS Tel 30 1d memory 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182242,DRX179864,CSUS Tel 30 1d memory 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182242,,,,1279740096.0,35548336.0,DRR189399,0:36,A:314850837;C:294188093;G:304654881;T:365946483;N:99802,36,,,,314850837,294188093,304654881,365946483,99802,DRX179864,DRS200400,DRA008864,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89485,,0.18205,,0.70593,,0.49333,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
106,DRR189398,DRX179863,DRS200399,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  30 min post test session of 1 day memory test in non trace 2 Way Active Avoidance coditioning 1,SAMD00182241,,sample name:CSUS Tel 30 1d memory 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182241,DRX179863,CSUS Tel 30 1d memory 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182241,,,,3012353100.0,83676475.0,DRR189398,0:36,A:740795057;C:693120664;G:717419185;T:860784745;N:233449,36,,,,740795057,693120664,717419185,860784745,233449,DRX179863,DRS200399,DRA008864,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89676,,0.1791,,0.70569,,0.49835,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
107,DRR189397,DRX179862,DRS200428,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post exposure to the conditioning tank 3,SAMD00182240,,sample name:Cont Tel 60 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182240,DRX179862,Cont Tel 60 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182240,,,,5590147750.0,111802955.0,DRR189397,0:50,A:1365131560;C:1269631295;G:1366791321;T:1588422020;N:171554,50,,,,1365131560,1269631295,1366791321,1588422020,171554,DRX179862,DRS200428,DRA008863,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89334,,0.16354,,0.7011,,0.49383,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
108,DRR189396,DRX179861,DRS200427,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post exposure to the conditioning tank 2,SAMD00182239,,sample name:Cont Tel 60 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182239,DRX179861,Cont Tel 60 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182239,,,,6429019650.0,128580393.0,DRR189396,0:50,A:1570141412;C:1457539089;G:1572785681;T:1828358007;N:195461,50,,,,1570141412,1457539089,1572785681,1828358007,195461,DRX179861,DRS200427,DRA008863,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89595,,0.16204,,0.70743,,0.49805,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
109,DRR189395,DRX179860,DRS200426,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post exposure to the conditioning tank 1,SAMD00182238,,sample name:Cont Tel 60 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182238,DRX179860,Cont Tel 60 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182238,,,,6644185850.0,132883717.0,DRR189395,0:50,A:1637322491;C:1498943556;G:1616212676;T:1891505597;N:201530,50,,,,1637322491,1498943556,1616212676,1891505597,201530,DRX179860,DRS200426,DRA008863,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89573,,0.16421,,0.7037,,0.49805,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
110,DRR189394,DRX179859,DRS200407,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light stimulation in the conditioning tank 3,SAMD00182237,,sample name:CS Tel 60 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182237,DRX179859,CS Tel 60 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182237,,,,1387078956.0,38529971.0,DRR189394,0:36,A:333990578;C:315361737;G:337599372;T:400057968;N:69301,36,,,,333990578,315361737,337599372,400057968,69301,DRX179859,DRS200407,DRA008862,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.88133,,0.18418,,0.70747,,0.4971,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
111,DRR189393,DRX179858,DRS200406,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light stimulation in the conditioning tank 2,SAMD00182236,,sample name:CS Tel 60 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182236,DRX179858,CS Tel 60 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182236,,,,537029424.0,14917484.0,DRR189393,0:36,A:127421487;C:122494467;G:132164579;T:154921150;N:27741,36,,,,127421487,122494467,132164579,154921150,27741,DRX179858,DRS200406,DRA008862,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.88264,,0.17793,,0.7083,,0.49123,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
112,DRR189392,DRX179857,DRS200405,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light stimulation in the conditioning tank 1,SAMD00182235,,sample name:CS Tel 60 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182235,DRX179857,CS Tel 60 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182235,,,,3163663656.0,87879546.0,DRR189392,0:36,A:766146692;C:714108562;G:771785405;T:911468887;N:154110,36,,,,766146692,714108562,771785405,911468887,154110,DRX179857,DRS200405,DRA008862,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.88114,,0.1803,,0.7052,,0.4917,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
113,DRR189391,DRX179856,DRS200404,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post electrical shock delivery in the conditioning tank 3,SAMD00182234,,sample name:US Tel 60 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182234,DRX179856,US Tel 60 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182234,,,,1535884704.0,42663464.0,DRR189391,0:36,A:367444721;C:350978310;G:375524359;T:441859454;N:77860,36,,,,367444721,350978310,375524359,441859454,77860,DRX179856,DRS200404,DRA008861,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.88103,,0.1788,,0.7082,,0.49462,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
114,DRR189390,DRX179855,DRS200403,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post electrical shock delivery in the conditioning tank 2,SAMD00182233,,sample name:US Tel 60 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182233,DRX179855,US Tel 60 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182233,,,,737309916.0,20480831.0,DRR189390,0:36,A:176982713;C:168284406;G:179343270;T:212662841;N:36686,36,,,,176982713,168284406,179343270,212662841,36686,DRX179855,DRS200403,DRA008861,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.87995,,0.18515,,0.70816,,0.49393,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
115,DRR189389,DRX179854,DRS200402,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post electrical shock delivery in the conditioning tank 1,SAMD00182232,,sample name:US Tel 60 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182232,DRX179854,US Tel 60 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182232,,,,595837404.0,16551039.0,DRR189389,0:36,A:143956004;C:134783754;G:145443580;T:171624939;N:29127,36,,,,143956004,134783754,145443580,171624939,29127,DRX179854,DRS200402,DRA008861,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.87682,,0.18328,,0.70309,,0.49081,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
116,DRR189388,DRX179853,DRS200452,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 3,SAMD00182231,,sample name:CSUS Tel 60 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182231,DRX179853,CSUS Tel 60 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182231,,,,608050044.0,16890279.0,DRR189388,0:36,A:145025778;C:137906052;G:149542672;T:175545338;N:30204,36,,,,145025778,137906052,149542672,175545338,30204,DRX179853,DRS200452,DRA008860,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.87983,,0.18602,,0.70445,,0.49195,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
117,DRR189387,DRX179852,DRS200451,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 2,SAMD00182230,,sample name:CSUS Tel 60 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182230,DRX179852,CSUS Tel 60 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182230,,,,777589452.0,21599707.0,DRR189387,0:36,A:185463269;C:177742981;G:190443063;T:223900096;N:40043,36,,,,185463269,177742981,190443063,223900096,40043,DRX179852,DRS200451,DRA008860,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.88331,,0.17918,,0.70516,,0.48956,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
118,DRR189386,DRX179851,DRS200450,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of adult zebrafrish  60 min post light and electrical shock association in non trace 2 Way Active Avoidance coditioning 1,SAMD00182229,,sample name:CSUS Tel 60 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182229,DRX179851,CSUS Tel 60 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182229,,,,2738622348.0,76072843.0,DRR189386,0:36,A:662989485;C:622023190;G:663013857;T:790459930;N:135886,36,,,,662989485,622023190,663013857,790459930,135886,DRX179851,DRS200450,DRA008860,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.87743,,0.19164,,0.70025,,0.49073,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
119,DRR189385,DRX179850,DRS200435,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of EMX3  /  adult zebrafish 3,SAMD00182228,,sample name:Emx3     Adult Tel 3|genotype:Emx3 / |tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182228,DRX179850,Emx3 /  Adult Tel 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182228,,,,1323636552.0,36767682.0,DRR189385,0:36,A:309582925;C:310206951;G:325673647;T:378136039;N:36990,36,,,,309582925,310206951,325673647,378136039,36990,DRX179850,DRS200435,DRA008859,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.8932,,0.19244,,0.71334,,0.50591,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
120,DRR189384,DRX179849,DRS200434,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of EMX3  /  adult zebrafish 2,SAMD00182227,,sample name:Emx3     Adult Tel 2|genotype:Emx3 / |tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182227,DRX179849,Emx3 /  Adult Tel 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182227,,,,2994105168.0,83169588.0,DRR189384,0:36,A:709730692;C:691531995;G:727245229;T:865514929;N:82323,36,,,,709730692,691531995,727245229,865514929,82323,DRX179849,DRS200434,DRA008859,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90382,,0.1826,,0.70197,,0.49719,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
121,DRR189383,DRX179848,DRS200433,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of EMX3  /  adult zebrafish 1,SAMD00182226,,sample name:Emx3     Adult Tel 1|genotype:Emx3 / |tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182226,DRX179848,Emx3 /  Adult Tel 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182226,,,,1151464896.0,31985136.0,DRR189383,0:36,A:272427216;C:266708394;G:280781178;T:331515997;N:32111,36,,,,272427216,266708394,280781178,331515997,32111,DRX179848,DRS200433,DRA008859,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89942,,0.17402,,0.70364,,0.49438,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
122,DRR189382,DRX179847,DRS200421,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of wild type adult zebrafish 3,SAMD00182225,,sample name:WT Adult Tel 3|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182225,DRX179847,WT Adult Tel 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182225,,,,2837488824.0,78819134.0,DRR189382,0:36,A:678395895;C:655098137;G:687520693;T:816395518;N:78581,36,,,,678395895,655098137,687520693,816395518,78581,DRX179847,DRS200421,DRA008858,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89483,,0.18623,,0.70544,,0.49839,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
123,DRR189381,DRX179846,DRS200420,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of wild type adult zebrafish 2,SAMD00182224,,sample name:WT Adult Tel 2|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182224,DRX179846,WT Adult Tel 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182224,,,,1456800264.0,40466674.0,DRR189381,0:36,A:345320431;C:336838149;G:356264798;T:418336552;N:40334,36,,,,345320431,336838149,356264798,418336552,40334,DRX179846,DRS200420,DRA008858,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89496,,0.18691,,0.70802,,0.49721,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
124,DRR189380,DRX179845,DRS200419,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Telencephalon of wild type adult zebrafish 1,SAMD00182223,,sample name:WT Adult Tel 1|genotype:wild type|tissue:brain,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182223,DRX179845,WT Adult Tel 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182223,,,,2533282452.0,70368957.0,DRR189380,0:36,A:602595083;C:585466052;G:616064286;T:729086926;N:70105,36,,,,602595083,585466052,616064286,729086926,70105,DRX179845,DRS200419,DRA008858,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89412,,0.19005,,0.70816,,0.49843,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Adult,Adult,Brain,Nervous System
125,DRR189379,DRX179844,DRS200410,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 3,SAMD00182222,,sample name:Emx3     Larva body 3|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182222,DRX179844,Emx3 /  Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182222,,,,1759409208.0,48872478.0,DRR189379,0:36,A:401147348;C:424523813;G:426350919;T:507310828;N:76300,36,,,,401147348,424523813,426350919,507310828,76300,DRX179844,DRS200410,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90975,,0.11439,,0.66076,,0.47775,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
126,DRR189378,DRX179843,DRS200409,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 2,SAMD00182221,,sample name:Emx3     Larva body 2|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182221,DRX179843,Emx3 /  Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182221,,,,1318201020.0,36616695.0,DRR189378,0:36,A:297850068;C:316786585;G:323717530;T:379789606;N:57231,36,,,,297850068,316786585,323717530,379789606,57231,DRX179843,DRS200409,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.9116,,0.11269,,0.65837,,0.46733,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
127,DRR189377,DRX179842,DRS200408,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 1,SAMD00182220,,sample name:Emx3     Larva body 1|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182220,DRX179842,Emx3 /  Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182220,,,,812483964.0,22568999.0,DRR189377,0:36,A:185173338;C:197790160;G:197482964;T:232000884;N:36618,36,,,,185173338,197790160,197482964,232000884,36618,DRX179842,DRS200408,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91107,,0.1171,,0.65981,,0.47458,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
128,DRR189376,DRX179841,DRS200449,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 3,SAMD00182219,,sample name:WT Larva body 3|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182219,DRX179841,WT Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182219,,,,4030038144.0,111945504.0,DRR189376,0:36,A:943709984;C:971756680;G:977594500;T:1136798448;N:178532,36,,,,943709984,971756680,977594500,1136798448,178532,DRX179841,DRS200449,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89574,,0.12331,,0.65831,,0.48096,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
129,DRR189375,DRX179840,DRS200448,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 2,SAMD00182218,,sample name:WT Larva body 2|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182218,DRX179840,WT Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182218,,,,1991670804.0,55324189.0,DRR189375,0:36,A:454367176;C:479012055;G:488407231;T:569793674;N:90668,36,,,,454367176,479012055,488407231,569793674,90668,DRX179840,DRS200448,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90911,,0.12455,,0.65494,,0.47971,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
130,DRR189374,DRX179839,DRS200447,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 1,SAMD00182217,,sample name:WT Larva body 1|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182217,DRX179839,WT Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182217,,,,1018340100.0,28287225.0,DRR189374,0:36,A:233370050;C:244140659;G:247795084;T:292989542;N:44765,36,,,,233370050,244140659,247795084,292989542,44765,DRX179839,DRS200447,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91078,,0.12578,,0.6524,,0.48016,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
174,DRR084198,DRX078029,DRS086523,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate2],SAMD00073605,,sample name:TES1 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073605,DRX078029,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073605,,,,1382763132.0,38410087.0,DRR084198,0:36,A:314367195;C:333340483;G:353519828;T:378654329;N:2881297,36,,,,314367195,333340483,353519828,378654329,2881297,DRX078029,DRS086523,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90366,,0.02033,,0.77104,,0.46543,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
175,DRR084197,DRX078028,DRS086522,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
176,DRR084196,DRX078027,DRS086521,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],SAMD00073603,,sample name:Et 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073603,DRX078027,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073603,,,,1456791660.0,40466435.0,DRR084196,0:36,A:336533534;C:355126203;G:368021063;T:394179246;N:2931614,36,,,,336533534,355126203,368021063,394179246,2931614,DRX078027,DRS086521,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89408,,0.02082,,0.77027,,0.45866,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
177,DRR084195,DRX078026,DRS086520,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],SAMD00073602,,sample name:O 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073602,DRX078026,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073602,,,,1627945092.0,45220697.0,DRR084195,0:36,A:381205209;C:392853175;G:410714269;T:439790560;N:3381879,36,,,,381205209,392853175,410714269,439790560,3381879,DRX078026,DRS086520,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89419,,0.02159,,0.76848,,0.46407,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
178,DRR084194,DRX078025,DRS086519,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate2],SAMD00073601,,sample name:DHP 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073601,DRX078025,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073601,,,,969680196.0,26935561.0,DRR084194,0:36,A:223558856;C:233793515;G:244712298;T:265549055;N:2066472,36,,,,223558856,233793515,244712298,265549055,2066472,DRX078025,DRS086519,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90178,,0.02203,,0.76579,,0.46491,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
179,DRR084193,DRX078024,DRS086518,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],SAMD00073600,,sample name:DES 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073600,DRX078024,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073600,,,,825301296.0,22925036.0,DRR084193,0:36,A:189771874;C:198593952;G:209666041;T:225480165;N:1789264,36,,,,189771874,198593952,209666041,225480165,1789264,DRX078024,DRS086518,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90036,,0.0197,,0.7721,,0.45773,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
180,DRR084192,DRX078023,DRS086517,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring late sample,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],SAMD00073599,,sample name:O|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073599,DRX078023,zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073599,,,,1474870356.0,40968621.0,DRR084192,0:36,A:334130826;C:361572335;G:369758908;T:409173431;N:234856,36,,,,334130826,361572335,369758908,409173431,234856,DRX078023,DRS086517,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91516,,0.02086,,0.76792,,0.47914,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
181,DRR084191,DRX078022,DRS086516,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
182,DRR084190,DRX078021,DRS086515,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo maturation inducing hormone DHP treatment,zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate1],SAMD00073597,,sample name:DHP|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073597,DRX078021,zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073597,,,,1527194556.0,42422071.0,DRR084190,0:36,A:352068936;C:371030475;G:383086948;T:420761508;N:246689,36,,,,352068936,371030475,383086948,420761508,246689,DRX078021,DRS086515,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91815,,0.02248,,0.76209,,0.46867,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
183,DRR084189,DRX078020,DRS086514,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo testosterone treatment,zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate1],SAMD00073596,,sample name:TES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073596,DRX078020,zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073596,,,,1403618796.0,38989411.0,DRR084189,0:36,A:321063874;C:342718133;G:352434647;T:387171455;N:230687,36,,,,321063874,342718133,352434647,387171455,230687,DRX078020,DRS086514,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91583,,0.02212,,0.76073,,0.47596,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
184,DRR084188,DRX078019,DRS086513,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo diethylstilbestrol DES treatment,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],SAMD00073595,,sample name:DES|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073595,DRX078019,zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073595,,,,1532053512.0,42557042.0,DRR084188,0:36,A:342701220;C:372650449;G:392432461;T:424025702;N:243680,36,,,,342701220,372650449,392432461,424025702,243680,DRX078019,DRS086513,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.91276,,0.01965,,0.77358,,0.46461,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
185,DRR084187,DRX078018,DRS086512,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,in vivo ethanol treatment,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],SAMD00073594,,sample name:EtOH|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073594,DRX078018,zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073594,,,,1152032724.0,32000909.0,DRR084187,0:36,A:265166034;C:279617628;G:285136940;T:321928656;N:183466,36,,,,265166034,279617628,285136940,321928656,183466,DRX078018,DRS086512,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.90791,,0.02405,,0.75972,,0.48931,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Adult,Adult,Gonad,Reproductive System
9874,ERR4132490,ERX4099806,ERS4552001,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R904,SAMEA6824372,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824372|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R904|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R904|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R904 s,R904 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R904_sr.fastq.gz,fastq,1605165390.0,31794192.0,E MTAB 9054:R904,0:50.49 1:0,A:412564740;C:388045945;G:374953342;T:427657902;N:1943461,50,0,,,412564740,388045945,374953342,427657902,1943461,ERX4099806,ERS4552001,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93893,,0.09893,,0.64646,,0.47809,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9875,ERR4132489,ERX4099805,ERS4552000,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R900,SAMEA6824371,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824371|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R900|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.6|sample name:E MTAB 9054:R900|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R900 s,R900 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R900_sr.fastq.gz,fastq,1597198644.0,31638370.0,E MTAB 9054:R900,0:50.48 1:0,A:410085529;C:386591071;G:373950085;T:424276623;N:2295336,50,0,,,410085529,386591071,373950085,424276623,2295336,ERX4099805,ERS4552000,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93876,,0.09801,,0.64889,,0.48057,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9876,ERR4132488,ERX4099804,ERS4551999,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R896,SAMEA6824370,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824370|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R896|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R896|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R896 s,R896 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R896_sr.fastq.gz,fastq,1946340744.0,38553341.0,E MTAB 9054:R896,0:50.48 1:0,A:497881336;C:472722708;G:455800573;T:517246014;N:2690113,50,0,,,497881336,472722708,455800573,517246014,2690113,ERX4099804,ERS4551999,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93904,,0.10115,,0.64885,,0.47903,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9877,ERR4132487,ERX4099803,ERS4551998,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R906,SAMEA6824369,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824369|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R906|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R906|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R906 s,R906 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R906_sr.fastq.gz,fastq,2341343751.0,46379726.0,E MTAB 9054:R906,0:50.48 1:0,A:597650493;C:569437401;G:551299383;T:619558551;N:3397923,50,0,,,597650493,569437401,551299383,619558551,3397923,ERX4099803,ERS4551998,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.94175,,0.09795,,0.65153,,0.47478,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9878,ERR4132486,ERX4099802,ERS4551997,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R902,SAMEA6824368,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824368|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R902|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R902|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R902 s,R902 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R902_sr.fastq.gz,fastq,1632244657.0,32331034.0,E MTAB 9054:R902,0:50.49 1:0,A:413710466;C:400183665;G:387130890;T:428954946;N:2264690,50,0,,,413710466,400183665,387130890,428954946,2264690,ERX4099802,ERS4551997,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.94282,,0.09186,,0.65192,,0.48446,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9879,ERR4132485,ERX4099801,ERS4551996,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R898,SAMEA6824367,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824367|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R898|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R898|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R898 s,R898 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R898_sr.fastq.gz,fastq,1973588979.0,39097363.0,E MTAB 9054:R898,0:50.48 1:0,A:501700006;C:481059078;G:466931881;T:520778140;N:3119874,50,0,,,501700006,481059078,466931881,520778140,3119874,ERX4099801,ERS4551996,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.94133,,0.09578,,0.651,,0.474,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9880,ERR4132484,ERX4099800,ERS4551995,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R903,SAMEA6824366,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824366|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R903|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R903|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R903 s,R903 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R903_sr.fastq.gz,fastq,1978975800.0,39199481.0,E MTAB 9054:R903,0:50.48 1:0,A:502614523;C:482986303;G:468168184;T:522608062;N:2598728,50,0,,,502614523,482986303,468168184,522608062,2598728,ERX4099800,ERS4551995,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.9404,,0.09216,,0.64607,,0.47417,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9881,ERR4132483,ERX4099799,ERS4551994,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R899,SAMEA6824365,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824365|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R899|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R899|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R899 s,R899 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R899_sr.fastq.gz,fastq,1556233879.0,30835141.0,E MTAB 9054:R899,0:50.47 1:0,A:394448696;C:380284673;G:367546543;T:410802983;N:3150984,50,0,,,394448696,380284673,367546543,410802983,3150984,ERX4099799,ERS4551994,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93845,,0.09509,,0.64926,,0.48436,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9882,ERR4132482,ERX4099798,ERS4551993,ERP121652,PRJEB38247,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E-MTAB-9054,Transcriptome Analysis,Endocrine disruption can trigger far reaching effects on environmental populations  justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU  CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing  30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input  read counts were normalized with DESeq2 for differential gene expression analysis.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5  99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R895,SAMEA6824364,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824364|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R895|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R895|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,E MTAB 9054:R895 s,R895 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019.  CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. 6 PTU 6 propyl 2 sulfanylidene 1H pyrimidin 4 one  CAS number 51 52 5    99% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121652,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11,R895_sr.fastq.gz,fastq,1098959757.0,21771883.0,E MTAB 9054:R895,0:50.48 1:0,A:281414032;C:266978094;G:257304686;T:291591340;N:1671605,50,0,,,281414032,266978094,257304686,291591340,1671605,ERX4099798,ERS4551993,ERA2597157,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93996,,0.09776,,0.64989,,0.47968,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-11,Larval,Larval,Whole Organism,All anatomical structures
9883,ERR4140034,ERX4107347,ERS4556110,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R86,SAMEA6828487,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828487|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R86|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R86|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R86 s,R86 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R86_sr.fastq.gz,fastq,1327826966.0,26294265.0,E MTAB 9056:R86,0:50.50 1:0,A:340934934;C:322947435;G:309801278;T:353159102;N:984217,50,0,,,340934934,322947435,309801278,353159102,984217,ERX4107347,ERS4556110,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.9393,,0.1031,,0.65683,,0.46848,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9884,ERR4140033,ERX4107346,ERS4556109,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R164,SAMEA6828486,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828486|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R164|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R164|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R164 s,R164 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R164_sr.fastq.gz,fastq,1513567439.0,29975869.0,E MTAB 9056:R164,0:50.49 1:0,A:388109813;C:368964600;G:352756505;T:402261160;N:1475361,50,0,,,388109813,368964600,352756505,402261160,1475361,ERX4107346,ERS4556109,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93992,,0.10282,,0.65437,,0.47367,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9885,ERR4140032,ERX4107345,ERS4556108,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R158,SAMEA6828485,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828485|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R158|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R158|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R158 s,R158 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R158_sr.fastq.gz,fastq,1512642153.0,29962837.0,E MTAB 9056:R158,0:50.48 1:0,A:389585690;C:365364747;G:351299223;T:404327286;N:2065207,50,0,,,389585690,365364747,351299223,404327286,2065207,ERX4107345,ERS4556108,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93757,,0.10553,,0.65557,,0.47147,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9886,ERR4140031,ERX4107344,ERS4556107,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R89,SAMEA6828484,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828484|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R89|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R89|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R89 s,R89 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R89_sr.fastq.gz,fastq,1347758243.0,26686154.0,E MTAB 9056:R89,0:50.50 1:0,A:347954623;C:326744319;G:311736057;T:360479809;N:843435,50,0,,,347954623,326744319,311736057,360479809,843435,ERX4107344,ERS4556107,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93909,,0.1032,,0.64906,,0.47499,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9887,ERR4140030,ERX4107343,ERS4556106,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R167,SAMEA6828483,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828483|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R167|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R167|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R167 s,R167 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R167_sr.fastq.gz,fastq,1422756236.0,28174340.0,E MTAB 9056:R167,0:50.50 1:0,A:366380887;C:345824655;G:330108682;T:379312527;N:1129485,50,0,,,366380887,345824655,330108682,379312527,1129485,ERX4107343,ERS4556106,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93724,,0.10506,,0.65001,,0.47599,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9888,ERR4140029,ERX4107342,ERS4556105,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R161,SAMEA6828482,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828482|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R161|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R161|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R161 s,R161 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R161_sr.fastq.gz,fastq,1696412529.0,33592555.0,E MTAB 9056:R161,0:50.50 1:0,A:439133160;C:409023953;G:389977077;T:457053986;N:1224353,50,0,,,439133160,409023953,389977077,457053986,1224353,ERX4107342,ERS4556105,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93609,,0.1083,,0.6535,,0.46658,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9889,ERR4140028,ERX4107341,ERS4556104,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R85,SAMEA6828481,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828481|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R85|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R85|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R85 s,R85 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1|Experimental Factor: dose:0,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R85_sr.fastq.gz,fastq,1115426084.0,22086160.0,E MTAB 9056:R85,0:50.50 1:0,A:288411880;C:265358022;G:259432943;T:301493661;N:729578,50,0,,,288411880,265358022,259432943,301493661,729578,ERX4107341,ERS4556104,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.94238,,0.10918,,0.65372,,0.48727,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9890,ERR4140027,ERX4107340,ERS4556103,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R162,SAMEA6828480,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828480|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R162|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R162|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R162 s,R162 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1|Experimental Factor: dose:0,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R162_sr.fastq.gz,fastq,1368462525.0,27098537.0,E MTAB 9056:R162,0:50.50 1:0,A:352965195;C:330975762;G:317956233;T:365598349;N:966986,50,0,,,352965195,330975762,317956233,365598349,966986,ERX4107340,ERS4556103,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93788,,0.10812,,0.65482,,0.47962,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
9891,ERR4140026,ERX4107339,ERS4556102,ERP121678,PRJEB38271,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,E-MTAB-9056,Transcriptome Analysis,The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3  CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE  high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,R157,SAMEA6828479,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany",ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828479|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology  Applied Ecology and Bioresources Division  Schmallenberg  Germany Institute of Ecology  Evolution and Diversity  Goethe University Frankfurt  Frankfurt am Main  Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R157|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R157|scientific name:Danio rerio|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups,E MTAB 9056:R157 s,R157 s,RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. T3 3 three prime 5 Triiodo L thyronine  CAS number 6893 02 3  95% purity was purchased from Merck KGgA Darmstadt  Germany. Test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark while being constantly aerated. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.  The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 40 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined through a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using RNApico© chips Agilent  5067 1513. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina.,Experimental Factor: compound:n1|Experimental Factor: dose:0,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP121678,Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13,R157_sr.fastq.gz,fastq,1500167669.0,29707076.0,E MTAB 9056:R157,0:50.50 1:0,A:386622926;C:363330639;G:347819057;T:401278075;N:1116972,50,0,,,386622926,363330639,347819057,401278075,1116972,ERX4107339,ERS4556102,ERA2597448,"Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive","Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive",1,0.93887,,0.10641,,0.65283,,0.46616,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2020-05-12,Larval,Larval,Whole Organism,All anatomical structures
10068,ERR4844843,ERX4714625,ERS5338302,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis  autophagy and cell cycle regulation  among others. Here we employ targeted morpholino knockdown to deplete Foxk1  Fokx2  and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation  characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],wt rep2,SAMEA7579966,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579966|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep2|strain:Ab / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep2 s,wt rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio.  1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep2.fastq.gz,fastq,3456340392.0,34221192.0,E MTAB 9777:wt rep2,0:101 1:0,A:850781866;C:827613239;G:837337477;T:936245388;N:4362422,101,0,,,850781866,827613239,837337477,936245388,4362422,ERX4714625,ERS5338302,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94198,,0.05681,,0.69613,,0.46685,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10069,ERR4844842,ERX4714624,ERS5338301,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis  autophagy and cell cycle regulation  among others. Here we employ targeted morpholino knockdown to deplete Foxk1  Fokx2  and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation  characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],wt rep1,SAMEA7579965,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579965|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep1 s,wt rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio.  1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep1.fastq.gz,fastq,5640822932.0,55849732.0,E MTAB 9777:wt rep1,0:101 1:0,A:1394470185;C:1346058952;G:1354472388;T:1538701573;N:7119834,101,0,,,1394470185,1346058952,1354472388,1538701573,7119834,ERX4714624,ERS5338301,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94371,,0.05678,,0.69664,,0.47233,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10070,ERR4844841,ERX4714623,ERS5338300,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis  autophagy and cell cycle regulation  among others. Here we employ targeted morpholino knockdown to deplete Foxk1  Fokx2  and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation  characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],foxk MO rep2,SAMEA7579964,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579964|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep2|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep2 s,foxk MO rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio.  1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep2.fastq.gz,fastq,3550070715.0,35149215.0,E MTAB 9777:foxk MO rep2,0:101 1:0,A:901160433;C:835963324;G:840839574;T:967604789;N:4502595,101,0,,,901160433,835963324,840839574,967604789,4502595,ERX4714623,ERS5338300,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94006,,0.07603,,0.69455,,0.46867,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10071,ERR4844840,ERX4714622,ERS5338299,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis  autophagy and cell cycle regulation  among others. Here we employ targeted morpholino knockdown to deplete Foxk1  Fokx2  and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation  characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],foxk MO rep1,SAMEA7579963,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579963|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep1 s,foxk MO rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl  0.005% CaCl2  0.0013% KCl  99.9557% H2O  0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio.  1c embryos were injected with morpholino oligonucleotides targeting foxk1  foxk2  and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen  Valencia  CA  USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina  San Diego  CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al.  High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011  940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep1.fastq.gz,fastq,3601987139.0,35663239.0,E MTAB 9777:foxk MO rep1,0:101 1:0,A:910641017;C:846039018;G:853351642;T:987409698;N:4545764,101,0,,,910641017,846039018,853351642,987409698,4545764,ERX4714622,ERS5338299,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.93784,,0.08061,,0.69292,,0.47364,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10072,ERR4910331,ERX4777154,ERS5435101,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R842,SAMEA7678119,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678119|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R842|age:96|batch:T10|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:10|sample name:E MTAB 9853:R842|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R842 s,R842 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:3|Experimental Factor: growth condition:high exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R842.fastq.gz,fastq,2078761529.0,41168286.0,E MTAB 9853:R842,0:50.49 1:0,A:525043812;C:513138389;G:493165128;T:542354255;N:5059945,50,0,,,525043812,513138389,493165128,542354255,5059945,ERX4777154,ERS5435101,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93137,,0.09995,,0.66634,,0.48015,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10073,ERR4910330,ERX4777153,ERS5435100,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R840,SAMEA7678118,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678118|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R840|age:96|batch:T10|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:10|sample name:E MTAB 9853:R840|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R840 s,R840 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:0.00075|Experimental Factor: growth condition:low exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R840.fastq.gz,fastq,2344231087.0,46394848.0,E MTAB 9853:R840,0:50.53 1:0,A:603829684;C:570903008;G:545594153;T:621405057;N:2499185,50,0,,,603829684,570903008,545594153,621405057,2499185,ERX4777153,ERS5435100,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.92792,,0.10519,,0.6646,,0.48351,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10074,ERR4910329,ERX4777152,ERS5435099,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R839,SAMEA7678117,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678117|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R839|age:96|batch:T10|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:10|sample name:E MTAB 9853:R839|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R839 s,R839 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: growth condition:normal,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R839.fastq.gz,fastq,1996290916.0,39508020.0,E MTAB 9853:R839,0:50.53 1:0,A:509362981;C:490497777;G:469414712;T:524505312;N:2510134,50,0,,,509362981,490497777,469414712,524505312,2510134,ERX4777152,ERS5435099,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93138,,0.10299,,0.66468,,0.48637,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10075,ERR4910328,ERX4777151,ERS5435098,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R838,SAMEA7678116,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678116|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R838|age:96|batch:T2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 9|sample name:E MTAB 9853:R838|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R838 s,R838 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:3|Experimental Factor: growth condition:high exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R838.fastq.gz,fastq,1801740137.0,35669320.0,E MTAB 9853:R838,0:50.51 1:0,A:466977493;C:436158087;G:416333880;T:479487201;N:2783476,50,0,,,466977493,436158087,416333880,479487201,2783476,ERX4777151,ERS5435098,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.92647,,0.11533,,0.666,,0.48331,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10076,ERR4910327,ERX4777150,ERS5435097,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R836,SAMEA7678115,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678115|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R836|age:96|batch:T2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 8|sample name:E MTAB 9853:R836|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R836 s,R836 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:0.00075|Experimental Factor: growth condition:low exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R836.fastq.gz,fastq,1816994468.0,35959155.0,E MTAB 9853:R836,0:50.53 1:0,A:465931946;C:444466278;G:425419784;T:479276121;N:1900339,50,0,,,465931946,444466278,425419784,479276121,1900339,ERX4777150,ERS5435097,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.92973,,0.10412,,0.66425,,0.4798,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10077,ERR4910326,ERX4777149,ERS5435096,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R835,SAMEA7678114,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678114|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R835|age:96|batch:T2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 9|sample name:E MTAB 9853:R835|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R835 s,R835 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: growth condition:normal,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R835.fastq.gz,fastq,2309123342.0,45698247.0,E MTAB 9853:R835,0:50.53 1:0,A:590448588;C:564838103;G:542833223;T:608521072;N:2482356,50,0,,,590448588,564838103,542833223,608521072,2482356,ERX4777149,ERS5435096,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.92963,,0.10535,,0.66156,,0.48118,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10078,ERR4910325,ERX4777148,ERS5435095,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R834,SAMEA7678113,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678113|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R834|age:96|batch:T11|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 8|sample name:E MTAB 9853:R834|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R834 s,R834 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:3|Experimental Factor: growth condition:high exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R834.fastq.gz,fastq,2122701060.0,42013381.0,E MTAB 9853:R834,0:50.52 1:0,A:547558397;C:515792741;G:494125094;T:562812656;N:2412172,50,0,,,547558397,515792741,494125094,562812656,2412172,ERX4777148,ERS5435095,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.92823,,0.11135,,0.66492,,0.48309,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10079,ERR4910324,ERX4777147,ERS5435094,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R832,SAMEA7678112,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678112|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R832|age:96|batch:T11|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 7|sample name:E MTAB 9853:R832|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R832 s,R832 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:chlorpyrifos|Experimental Factor: dose:0.00075|Experimental Factor: growth condition:low exposure,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R832.fastq.gz,fastq,2407016662.0,47713826.0,E MTAB 9853:R832,0:50.45 1:0,A:637497754;C:575428535;G:531202727;T:659395837;N:3491809,50,0,,,637497754,575428535,531202727,659395837,3491809,ERX4777147,ERS5435094,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.91708,,0.12568,,0.65494,,0.48103,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10080,ERR4910323,ERX4777146,ERS5435093,ERP125509,PRJEB41694,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E-MTAB-9853,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Chlorpyrifos CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Chlorpyrifos post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.75 mg/L  high exposure HE  3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for data normalization and differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R831,SAMEA7678111,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678111|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9853:R831|age:96|batch:T11|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:09.12.2019|genotype:wild type genotype|organism part:whole organism|rin:9 9|sample name:E MTAB 9853:R831|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,E MTAB 9853:R831 s,R831 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,Catalogue no. 2921 88 2. For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Chlorpyrifos CAS 2921 88 2  PESTANAL® analytical standard was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: growth condition:normal,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125509,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Chlorpyrifos below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R831.fastq.gz,fastq,2084924019.0,41265710.0,E MTAB 9853:R831,0:50.52 1:0,A:529532094;C:513298404;G:493028485;T:546325575;N:2739461,50,0,,,529532094,513298404,493028485,546325575,2739461,ERX4777146,ERS5435093,ERA3184347,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93121,,0.10702,,0.66064,,0.47779,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10081,ERR4910712,ERX4777535,ERS5435303,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R249,SAMEA7678322,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678322|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R249|age:96|batch:T14 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:18.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 7|sample name:E MTAB 9852:R249|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R249 s,R249 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:mid exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00022,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p823sR249_sr.fastq.gz,fastq,1238386140.0,24550785.0,E MTAB 9852:R249,0:50.44 1:0,A:315619803;C:300278943;G:290065564;T:328018594;N:4403236,50,0,,,315619803,300278943,290065564,328018594,4403236,ERX4777535,ERS5435303,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94195,,0.10394,,0.65249,,0.46521,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10082,ERR4910711,ERX4777534,ERS5435302,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R243,SAMEA7678321,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678321|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R243|age:96|batch:T8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 8|sample name:E MTAB 9852:R243|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R243 s,R243 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:mid exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00022,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p823sR243_sr.fastq.gz,fastq,2421445373.0,47945201.0,E MTAB 9852:R243,0:50.50 1:0,A:644050981;C:566576386;G:556332105;T:652514946;N:1970955,50,0,,,644050981,566576386,556332105,652514946,1970955,ERX4777534,ERS5435302,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93336,,0.11777,,0.64881,,0.47801,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10083,ERR4910710,ERX4777533,ERS5435301,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R237,SAMEA7678320,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678320|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R237|age:96|batch:T6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:10|sample name:E MTAB 9852:R237|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R237 s,R237 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:mid exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00022,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p823sR237_sr.fastq.gz,fastq,1226270967.0,24309553.0,E MTAB 9852:R237,0:50.44 1:0,A:315571166;C:295129287;G:284455226;T:326832027;N:4283261,50,0,,,315571166,295129287,284455226,326832027,4283261,ERX4777533,ERS5435301,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.941,,0.11242,,0.65504,,0.47821,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10084,ERR4910709,ERX4777532,ERS5435300,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R248,SAMEA7678319,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678319|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R248|age:96|batch:T14 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:18.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 4|sample name:E MTAB 9852:R248|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R248 s,R248 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:low exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00011,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR248_sr.fastq.gz,fastq,1418368154.0,28100223.0,E MTAB 9852:R248,0:50.48 1:0,A:365721817;C:343904004;G:327397507;T:379298412;N:2046414,50,0,,,365721817,343904004,327397507,379298412,2046414,ERX4777532,ERS5435300,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93616,,0.10439,,0.65502,,0.47312,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10085,ERR4910708,ERX4777531,ERS5435299,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R242,SAMEA7678318,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678318|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R242|age:96|batch:T8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:10|sample name:E MTAB 9852:R242|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R242 s,R242 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:low exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00011,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR242_sr.fastq.gz,fastq,1078378173.0,21357646.0,E MTAB 9852:R242,0:50.49 1:0,A:279746568;C:260936637;G:248227414;T:288521601;N:945953,50,0,,,279746568,260936637,248227414,288521601,945953,ERX4777531,ERS5435299,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9353,,0.11226,,0.6552,,0.47905,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10086,ERR4910707,ERX4777530,ERS5435298,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R236,SAMEA7678317,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678317|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R236|age:96|batch:T6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:10|sample name:E MTAB 9852:R236|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R236 s,R236 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:low exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00011,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR236_sr.fastq.gz,fastq,1095647196.0,21699085.0,E MTAB 9852:R236,0:50.49 1:0,A:284611814;C:265266246;G:251286658;T:293543067;N:939411,50,0,,,284611814,265266246,251286658,293543067,939411,ERX4777530,ERS5435298,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93368,,0.11269,,0.65748,,0.47474,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10087,ERR4910706,ERX4777529,ERS5435297,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R250,SAMEA7678316,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678316|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R250|age:96|batch:T14 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:18.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 3|sample name:E MTAB 9852:R250|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R250 s,R250 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:high exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00044,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR250_sr.fastq.gz,fastq,1360394339.0,26941236.0,E MTAB 9852:R250,0:50.49 1:0,A:350782395;C:329394637;G:315556205;T:363589748;N:1071354,50,0,,,350782395,329394637,315556205,363589748,1071354,ERX4777529,ERS5435297,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93459,,0.1084,,0.65612,,0.46181,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10088,ERR4910705,ERX4777528,ERS5435296,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R245,SAMEA7678315,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678315|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R245|age:96|batch:T8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 6|sample name:E MTAB 9852:R245|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R245 s,R245 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:high exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00044,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR245_sr.fastq.gz,fastq,4133671592.0,81841196.0,E MTAB 9852:R245,0:50.51 1:0,A:1069364626;C:992843654;G:956238531;T:1113501572;N:1723209,50,0,,,1069364626,992843654,956238531,1113501572,1723209,ERX4777528,ERS5435296,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93652,,0.11134,,0.65196,,0.4699,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10089,ERR4910704,ERX4777527,ERS5435295,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R239,SAMEA7678314,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678314|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R239|age:96|batch:T6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 8|sample name:E MTAB 9852:R239|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R239 s,R239 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:high exposure|Experimental Factor: compound:abamectin|Experimental Factor: dose:0.00044,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR239_sr.fastq.gz,fastq,1265182243.0,25065223.0,E MTAB 9852:R239,0:50.48 1:0,A:328276812;C:305137622;G:290542708;T:339548031;N:1677070,50,0,,,328276812,305137622,290542708,339548031,1677070,ERX4777527,ERS5435295,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93333,,0.11548,,0.65354,,0.47419,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10090,ERR4910703,ERX4777526,ERS5435294,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R247,SAMEA7678313,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678313|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R247|age:96|batch:T14 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:18.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 7|sample name:E MTAB 9852:R247|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R247 s,R247 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:normal|Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR247_sr.fastq.gz,fastq,1537094317.0,30449470.0,E MTAB 9852:R247,0:50.48 1:0,A:378609932;C:387657971;G:375197386;T:392878686;N:2750342,50,0,,,378609932,387657971,375197386,392878686,2750342,ERX4777526,ERS5435294,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94344,,0.08094,,0.66093,,0.47759,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10091,ERR4910702,ERX4777525,ERS5435293,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R241,SAMEA7678312,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678312|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R241|age:96|batch:T8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:9 7|sample name:E MTAB 9852:R241|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R241 s,R241 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:normal|Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p823sR241_sr.fastq.gz,fastq,1421173155.0,28241274.0,E MTAB 9852:R241,0:50.32 1:0,A:352339224;C:349259614;G:337822083;T:368520360;N:13231874,50,0,,,352339224,349259614,337822083,368520360,13231874,ERX4777525,ERS5435293,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94609,,0.08553,,0.65729,,0.47079,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10092,ERR4910701,ERX4777524,ERS5435292,ERP125510,PRJEB41695,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E-MTAB-9852,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of Abamectin CAS 71751 41 2. Abamectin is a heavily used insecticide applied for crop protection against sucking insects i.e. Acari. The Insecticide Resistance Action Committee IRAC classified Abamectin post its mode of action MoA in the target organism as a Glutamate gated chloride channel GluCl allosteric modulator Group 6. In vertebrates  GluCl do not exist  but they are closely related to vertebrate glycine receptors Wolstenholme 2012. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.11 mg/L  mid exposure ME  0.22 mg/L  high exposure HE  0.44 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R235,SAMEA7678311,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678311|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9852:R235|age:96|batch:T6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|extraction date:11.02.2019|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|rin:10|sample name:E MTAB 9852:R235|sex:mixed|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,E MTAB 9852:R235 s,R235 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. CASRN: 71751 41 2 Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Abamectin CAS: 71751 41 2  PESTANAL© analytical grade was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”.   The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: growth condition:normal|Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125510,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,p689sR235_sr.fastq.gz,fastq,1260969924.0,24967845.0,E MTAB 9852:R235,0:50.50 1:0,A:321334927;C:309076905;G:296926662;T:332736920;N:894510,50,0,,,321334927,309076905,296926662,332736920,894510,ERX4777524,ERS5435292,ERA3184562,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94005,,0.10804,,0.66014,,0.48173,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10093,ERR4910723,ERX4777546,ERS5435312,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R852,SAMEA7678331,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678331|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R852|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:low exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.000075|organism part:whole organism|pooled individuals:10|rin:9.2|sample name:E MTAB 9854:R852|sex:mixed|strain:AB|tank spawning group:T12,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R852 s,R852 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.075,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R852.fastq.gz,fastq,1501461841.0,29758462.0,E MTAB 9854:R852,0:50.45 1:0,A:383178331;C:363921609;G:352164753;T:397820217;N:4376931,50,0,,,383178331,363921609,352164753,397820217,4376931,ERX4777546,ERS5435312,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94338,,0.10128,,0.65161,,0.47039,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10094,ERR4910722,ERX4777545,ERS5435311,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R848,SAMEA7678330,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678330|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R848|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:low exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.000075|organism part:whole organism|pooled individuals:10|rin:9.1|sample name:E MTAB 9854:R848|sex:mixed|strain:AB|tank spawning group:T11,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R848 s,R848 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.075,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R848.fastq.gz,fastq,1270434813.0,25300616.0,E MTAB 9854:R848,0:50.21 1:0,A:323517980;C:302337722;G:291425285;T:335522576;N:17631250,50,0,,,323517980,302337722,291425285,335522576,17631250,ERX4777545,ERS5435311,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93466,,0.10517,,0.65425,,0.48408,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10095,ERR4910721,ERX4777544,ERS5435310,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R844,SAMEA7678329,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678329|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R844|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:low exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.000075|organism part:whole organism|pooled individuals:10|rin:9.7|sample name:E MTAB 9854:R844|sex:mixed|strain:AB|tank spawning group:T10,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R844 s,R844 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.075,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R844.fastq.gz,fastq,1617418458.0,32083973.0,E MTAB 9854:R844,0:50.41 1:0,A:414770839;C:390980511;G:372715594;T:431908857;N:7042657,50,0,,,414770839,390980511,372715594,431908857,7042657,ERX4777544,ERS5435310,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93517,,0.11298,,0.64999,,0.48035,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10096,ERR4910720,ERX4777543,ERS5435309,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R854,SAMEA7678328,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678328|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R854|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:high exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.0003|organism part:whole organism|pooled individuals:10|rin:9.8|sample name:E MTAB 9854:R854|sex:mixed|strain:AB|tank spawning group:T12,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R854 s,R854 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.3,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R854.fastq.gz,fastq,1673652816.0,33145949.0,E MTAB 9854:R854,0:50.49 1:0,A:424673752;C:411510497;G:395090177;T:440173524;N:2204866,50,0,,,424673752,411510497,395090177,440173524,2204866,ERX4777543,ERS5435309,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.94329,,0.09755,,0.65642,,0.4654,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10097,ERR4910719,ERX4777542,ERS5435308,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R850,SAMEA7678327,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678327|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R850|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:high exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.0003|organism part:whole organism|pooled individuals:10|rin:9.2|sample name:E MTAB 9854:R850|sex:mixed|strain:AB|tank spawning group:T11,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R850 s,R850 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.3,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R850.fastq.gz,fastq,2896828206.0,57502950.0,E MTAB 9854:R850,0:50.38 1:0,A:733652981;C:704288937;G:676740479;T:762532101;N:19613708,50,0,,,733652981,704288937,676740479,762532101,19613708,ERX4777542,ERS5435308,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93972,,0.1116,,0.65504,,0.47885,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures
10098,ERR4910718,ERX4777541,ERS5435307,ERP125511,PRJEB41696,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E-MTAB-9854,Transcriptome Analysis,The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish Danio rerio embryos as aquatic vertebrate non target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil CAS 2921 88 2. The Insecticide Resistance Action Committee IRAC classified Fipronil post its mode of action MoA in the target organism as an acetylcholinesterase AChE inhibitor Group 1B. The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events KE explaining upstream adverse effects in aquatic non target organisms. This will provide useful information to refine and improve existing adverse outcome pathways AOP. Furthermore  integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects  based on similarly altered transcriptomic and proteomic profiles.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for xxx hours under semi static conditions. Each test comprised of a low exposure LE  0.075 mg/L  high exposure HE  0.3 mg/L and negative control NC group and was performed in triplicates. At 96 hpf  10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode  producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,,Protocols: For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature. From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,R846,SAMEA7678326,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany",ENA first public:2021 10 15|ENA last update:2021 10 15|External Id:SAMEA7678326|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany Evolutionary Ecology and Environmental Toxicology  Faculty Biological Sciences  Goethe University Frankfurt  Frankfurt  Germany|INSDC first public:2021 10 15T00:15:29Z|INSDC last update:2021 10 15T00:15:29Z|INSDC status:public|Submitter Id:E MTAB 9854:R846|age:96|broker name:ArrayExpress|cas:120068 37 3|common name:zebrafish|condition:high exposure|developmental stage:larval stage|extraction date:27.01.2020|genotype:wild type genotype|nominal conc:0.0003|organism part:whole organism|pooled individuals:10|rin:9|sample name:E MTAB 9854:R846|sex:mixed|strain:AB|tank spawning group:T10,,,,,,,,,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,E MTAB 9854:R846 s,R846 s,mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,For each sample  10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction.  For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control  Low exposure  High exposure. Embryos were incubated at 27 +/  1°C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf  overall survival  hatch rates  morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh  aerated test solutions. At 96 hpf again  overall survival  hatch rates  morphological malformations and physiological changes were recorded before RNA and protein extraction. Fipronil CAS 120068 37 3  TraceCERT® was purchased from Merck KGgA Darmstadt  Germany. For the test solution preparation  first a high concentrated stock solution was prepared in Acetone 99.9% MS grade. From this stock  respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle and filled up with pure Acetone to a final volume of 1 ml. To the bottle for the control solution only 1ml of pure Acetone was added. The solvent was then evaporated at room temperature until no Acetone was left in the bottles. At last  200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  15 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. The pooled larvae in RP1 buffer were transferred to a screw cap eppendorf filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals  6004500 at room temperature.  From here on total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit Macherey Nagel  740933.250 according to the manufacturer's protocol.  RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit© Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.,Experimental Factor: compound:fipronil|Experimental Factor: dose:0.3,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP125511,Illumina HiSeq 4000 sequencing; mRNA Seq of zebrafish embryos 96hpf exposed to different concentrations of Fipronil below acute toxicity levels against untreated control groups,ENA FIRST PUBLIC:2021 10 15|ENA LAST UPDATE:2021 10 15,R846.fastq.gz,fastq,1287980321.0,25537756.0,E MTAB 9854:R846,0:50.43 1:0,A:327403451;C:313312050;G:302396862;T:339963183;N:4904775,50,0,,,327403451,313312050,302396862,339963183,4904775,ERX4777541,ERS5435307,ERA3184565,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93976,,0.11403,,0.6536,,0.48517,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2021-10-15,Larval,Larval,Whole Organism,All anatomical structures