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
14,DRR334977,DRX323973,DRS217313,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 3,SAMD00422597,,sample name:rRNA mock community 28 degrees rep 3|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422597,DRX323973,t28 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422597,,,,3791170746.0,37701921.0,DRR334977,0:100.56 1:0,A:967477491;C:926887571;G:898697642;T:998107868;N:174,100,0,,,967477491,926887571,898697642,998107868,174,DRX323973,DRS217313,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.31527,,0.06446,,0.88844,,0.62118,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
15,DRR334976,DRX323972,DRS217312,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 2,SAMD00422596,,sample name:rRNA mock community 28 degrees rep 2|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422596,DRX323972,t28 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422596,,,,2801693695.0,27860658.0,DRR334976,0:100.56 1:0,A:700189496;C:702936549;G:679920984;T:718646067;N:599,100,0,,,700189496,702936549,679920984,718646067,599,DRX323972,DRS217312,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.43508,,0.08819,,0.85859,,0.69447,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
16,DRR334975,DRX323971,DRS217311,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 28 degrees rep 1,SAMD00422595,,sample name:rRNA mock community 28 degrees rep 1|biological replicate:3|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:28|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422595,DRX323971,t28 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422595,,,,3148691934.0,31307464.0,DRR334975,0:100.57 1:0,A:785000734;C:791315678;G:766594599;T:805780465;N:458,100,0,,,785000734,791315678,766594599,805780465,458,DRX323971,DRS217311,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.37139,,0.09061,,0.94065,,0.74047,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
17,DRR334974,DRX323970,DRS217310,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 3,SAMD00422594,,sample name:rRNA mock community 19 degrees rep 3|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422594,DRX323970,t19 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422594,,,,2856186273.0,28400524.0,DRR334974,0:100.57 1:0,A:695685787;C:733754277;G:715270279;T:711475544;N:386,100,0,,,695685787,733754277,715270279,711475544,386,DRX323970,DRS217310,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.48152,,0.10933,,0.87105,,0.7287,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
18,DRR334973,DRX323969,DRS217309,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 2,SAMD00422593,,sample name:rRNA mock community 19 degrees rep 2|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422593,DRX323969,t19 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422593,,,,3199929804.0,31816971.0,DRR334973,0:100.57 1:0,A:777149590;C:825478743;G:804835148;T:792466124;N:199,100,0,,,777149590,825478743,804835148,792466124,199,DRX323969,DRS217309,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.4418,,0.10282,,0.89706,,0.74667,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
19,DRR334972,DRX323968,DRS217308,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 19 degrees rep 1,SAMD00422592,,sample name:rRNA mock community 19 degrees rep 1|biological replicate:2|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:19|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422592,DRX323968,t19 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422592,,,,3658675391.0,36374718.0,DRR334972,0:100.58 1:0,A:879342063;C:954687406;G:929537615;T:895107890;N:417,100,0,,,879342063,954687406,929537615,895107890,417,DRX323968,DRS217308,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.49439,,0.11691,,0.88239,,0.73925,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
20,DRR334971,DRX323967,DRS217307,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 3,SAMD00422591,,sample name:rRNA mock community 10 degrees rep 3|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:3|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422591,DRX323967,t10 3 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422591,,,,3017524690.0,30006334.0,DRR334971,0:100.56 1:0,A:771967717;C:738814269;G:712866126;T:793876235;N:343,100,0,,,771967717,738814269,712866126,793876235,343,DRX323967,DRS217307,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.33157,,0.07363,,0.9093,,0.73422,,100,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
21,DRR334970,DRX323966,DRS217306,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 2,SAMD00422590,,sample name:rRNA mock community 10 degrees rep 2|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:2|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422590,DRX323966,t10 2 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422590,,,,3115915184.0,30982336.0,DRR334970,0:100.57 1:0,A:765727966;C:794741415;G:771082024;T:784363609;N:170,100,0,,,765727966,794741415,771082024,784363609,170,DRX323966,DRS217306,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.45458,,0.10504,,0.89357,,0.749,,100,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
22,DRR334969,DRX323965,DRS217305,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.,,,totalRNA metatranscriptomic sequences from mock communities consist of five model species,rRNA mock community at 10 degrees rep 1,SAMD00422589,,sample name:rRNA mock community 10 degrees rep 1|biological replicate:1|collection date:2021 01 15|dev stage:Adult|technical replicate:1|temp:10|treatment:rRNA,,,,,,,,,NextSeq 2000 sequencing of SAMD00422589,DRX323965,t10 1 tRNA.fastq,1,NEBNext Kit for Illumina,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,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 SAMD00422589,,,,3206657309.0,31883532.0,DRR334969,0:100.57 1:0,A:792874386;C:814578518;G:787469614;T:811734581;N:210,100,0,,,792874386,814578518,787469614,811734581,210,DRX323965,DRS217305,DRA013226,"SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica","SINICA|Machida Laboratory Biodiversity Research Center, Academia Sinica",1,0.40156,,0.09664,,0.92898,,0.74114,,101,,B,,usable mapping rate,illumina,nextseq_v2,unknown,random_priming,nebnext,bulk,unknown,unknown,,Taiwan,2021-12-23,Adult,Adult,Undetermined,Undetermined
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
9918,ERR5059480,ERX4865549,ERS5523939,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,aAM 6h rep1,JD AD30 PRPN1970901,,ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-AD30_PRPN197090.tar.gz,nanopore,3739882337.0,3148027.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1,0:1188.01,A:1054501690;C:834193435;G:847423060;T:1003764152;N:0,1188,,,,1054501690,834193435,847423060,1003764152,0,ERX4865549,ERS5523939,ERA3206712,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,B,,usable mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9920,ERR4330695,ERX4277529,ERS4811113,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 2h rep1,WT 2h rep1,SAMEA7050483,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-B2_PDBN005727.tar.gz,fastq,,,ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1,,,,,,,,,,,,ERX4277529,,ERA2767154,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9921,ERR4327134,ERX4273968,ERS4808634,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 4h rep2,WT 4h rep2,SAMEA7048000,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-AM39_PDBN042841.tar.gz,nanopore,719646261.0,897768.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1,0:801.59,A:210217908;C:152963718;G:157393834;T:199070801;N:0,801,,,,210217908,152963718,157393834,199070801,0,ERX4273968,ERS4808634,ERA2764800,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,T,,under 1.2% mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9922,ERR4330696,ERX4277530,ERS4811114,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 4h rep1,WT 4h rep1,JD C3 PDBN006177,,ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-C3_PDBN006177.tar.gz,nanopore,4240799932.0,4331689.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2,0:979.02,A:1229803846;C:914476674;G:943703560;T:1152815852;N:0,979,,,,1229803846,914476674,943703560,1152815852,0,ERX4277530,ERS4811114,ERA2767154,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,B,,usable mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9923,ERR4327135,ERX4273969,ERS4808635,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 6h rep1,WT 6h rep1,JD AC29 PDBN024889,,ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-AC29_PDBN024889.tar.gz,nanopore,1900324756.0,2013035.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2,0:944.01,A:549431032;C:411510218;G:422103800;T:517279706;N:0,944,,,,549431032,411510218,422103800,517279706,0,ERX4273969,ERS4808635,ERA2764800,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,T,,long read,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9924,ERR4326350,ERX4273208,ERS4808398,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,430 LNA 6h rep1,430 LNA 6h rep1,SAMEA7047764,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-H8_PDBN059569.tar.gz,nanopore,722817654.0,657296.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1,0:1099.68,A:206996491;C:157022109;G:155085437;T:203713617;N:0,1099,,,,206996491,157022109,155085437,203713617,0,ERX4273208,ERS4808398,ERA2764399,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,T,,under 1.2% mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9925,ERR4335436,ERX4282181,ERS4818366,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 6h rep2,WT 6h rep2,JD W23 PRPN039928,,ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-W23_PRPN039928.tar.gz,nanopore,1268761319.0,1385621.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1,0:915.66,A:366823862;C:275507684;G:284634548;T:341795225;N:0,915,,,,366823862,275507684,284634548,341795225,0,ERX4282181,ERS4818366,ERA2769006,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,T,,under 1.2% mapping rate,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
9926,ERR4321680,ERX4268538,ERS4808125,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,WT 0h rep1,WT 0h rep1,JD A1 GDDN003032,,ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,GridION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,GridION,,ERP122761,GridION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,JD-A1_GDDN003032.tar.gz,nanopore,753417826.0,698774.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1,0:1078.20,A:214525685;C:165042952;G:171160615;T:202688574;N:0,1078,,,,214525685,165042952,171160615,202688574,0,ERX4268538,ERS4808125,ERA2763718,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,T,,long read,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Undetermined,Undetermined,Undetermined,Undetermined
30658,SRR28054753,SRX23704452,SRS20534448,SRP491086,PRJNA1078753,Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1230,,library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,High 3,H 3,H 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz,fastq fastq,6117817800.0,20392726.0,S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz,0:150 1:150,A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211,150,150,,,1635728688,1405168032,1464072107,1612834762,14211,SRX23704452,SRS20534448,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined
34961,SRR32588718,SRX27895233,SRS24266235,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F IE,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:inner ear|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from inner ear,C2 F2 F IE,C2 F2 F IE,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_152521_s2.skera.flnc.fastq.gz,fastq,93609779073.0,46650644.0,m84270 240904 152521 s2.skera.flnc.fastq.gz,0:2006.61,A:27359819621;C:19471270902;G:20218480457;T:26560208093;N:0,2006,,,,27359819621,19471270902,20218480457,26560208093,0,SRX27895233,SRS24266235,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Undetermined,Undetermined
36504,SRR535848,SRX174964,SRS352998,SRP014772,PRJNA172016,Danio rerio strain:*AB Variation,PRJNA172016,Other,Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.,,,RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox20 was created from 20 pooled hoxb1bb1219 fish that were the siblings of wt20.,Miller hox20.bam,Miller hox20.bam,,,,,,,,,,,Miller hox20.bam,Miller hox20.bam,1,50 bp Paired End,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</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>,SRP014772,,,hox20.bam,bam,2051648571.0,22151528.0,Miller hox20.bam,0:49 1:49,A:528770281;C:501621137;G:487051170;T:534176088;N:29895,49,49,,,528770281,501621137,487051170,534176088,29895,SRX174964,SRS352998,SRA056859,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.9629,0.96282,0.07314,0.07288,0.6714,0.67125,0.4665,0.4637,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2012-11-30,Undetermined,Undetermined,Undetermined,Undetermined
36739,SRR867022,SRX286270,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat,Danio rerio boot,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<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>,SRP022549,,,s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta,SOLiD_native SOLiD_native,9801985250.0,196039705.0,Zebrafish DV patterning Boot,0:50,0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939,50,,,,,,,,,SRX286270,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.59289,,0.09435,,0.92669,,0.7658,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36740,SRR867023,SRX286271,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  ICH,Danio rerio ICH,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,<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>,SRP022549,,,s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual,SOLiD_native SOLiD_native,10810535400.0,216210708.0,Zebrafish DV patterning ICH,0:50,0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417,50,,,,,,,,,SRX286271,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.42474,,0.06136,,0.93434,,0.75757,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
37961,SRR1205174,SRX501301,SRS582373,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 3,GSM1357182,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357182,GSM1357182: cntl neo 5hr 3; Danio rerio; RNA Seq,GSM1357182,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357182,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_3.fastq.gz,fastq,1630216750.0,32604335.0,GSM1357182 r1,0:50 1:0,A:435441738;C:384703554;G:377838654;T:432163463;N:69341,50,0,,,435441738,384703554,377838654,432163463,69341,SRX501301,SRS582373,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93632,,0.20492,,0.67551,,0.50281,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37962,SRR1205173,SRX501300,SRS582372,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 2,GSM1357181,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357181,GSM1357181: cntl neo 5hr 2; Danio rerio; RNA Seq,GSM1357181,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357181,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_2.fastq.gz,fastq,1812797550.0,36255951.0,GSM1357181 r1,0:50 1:0,A:484800524;C:426109547;G:417833682;T:483968870;N:84927,50,0,,,484800524,426109547,417833682,483968870,84927,SRX501300,SRS582372,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93602,,0.21513,,0.67517,,0.49404,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37963,SRR1205172,SRX501299,SRS582371,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 5hr 1,GSM1357180,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 5hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357180,GSM1357180: cntl neo 5hr 1; Danio rerio; RNA Seq,GSM1357180,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357180,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_5_1.fastq.gz,fastq,1616736500.0,32334730.0,GSM1357180 r1,0:50 1:0,A:425328931;C:388105733;G:379129548;T:424100489;N:71799,50,0,,,425328931,388105733,379129548,424100489,71799,SRX501299,SRS582371,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.9361,,0.23516,,0.68091,,0.50961,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37964,SRR1205171,SRX501298,SRS582370,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 3,GSM1357179,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357179,GSM1357179: gfp neo 5hr 3; Danio rerio; RNA Seq,GSM1357179,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357179,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_3.fastq.gz,fastq,1856512100.0,37130242.0,GSM1357179 r1,0:50 1:0,A:492227117;C:440944515;G:431529818;T:491731276;N:79374,50,0,,,492227117,440944515,431529818,491731276,79374,SRX501298,SRS582370,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93677,,0.28732,,0.71435,,0.50496,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37965,SRR1205170,SRX501297,SRS582369,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 2,GSM1357178,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357178,GSM1357178: gfp neo 5hr 2; Danio rerio; RNA Seq,GSM1357178,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357178,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_2.fastq.gz,fastq,1605154400.0,32103088.0,GSM1357178 r1,0:50 1:0,A:431076570;C:373656204;G:367046732;T:433299718;N:75176,50,0,,,431076570,373656204,367046732,433299718,75176,SRX501297,SRS582369,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93022,,0.29198,,0.69656,,0.47675,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37966,SRR1205169,SRX501296,SRS582368,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 5hr 1,GSM1357177,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 5hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:5hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357177,GSM1357177: gfp neo 5hr 1; Danio rerio; RNA Seq,GSM1357177,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357177,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_5_1.fastq.gz,fastq,1902899900.0,38057998.0,GSM1357177 r1,0:50 1:0,A:511489376;C:443148505;G:433716076;T:514461324;N:84619,50,0,,,511489376,443148505,433716076,514461324,84619,SRX501296,SRS582368,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.92977,,0.29647,,0.69583,,0.48582,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37967,SRR1205168,SRX501295,SRS582367,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 3,GSM1357176,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357176,GSM1357176: cntl neo 3hr 3; Danio rerio; RNA Seq,GSM1357176,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357176,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_3.fastq.gz,fastq,1555198750.0,31103975.0,GSM1357176 r1,0:50 1:0,A:416734314;C:365733903;G:359113904;T:413549150;N:67479,50,0,,,416734314,365733903,359113904,413549150,67479,SRX501295,SRS582367,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93432,,0.21789,,0.67363,,0.49063,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37968,SRR1205167,SRX501294,SRS582366,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 2,GSM1357175,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357175,GSM1357175: cntl neo 3hr 2; Danio rerio; RNA Seq,GSM1357175,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357175,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_2.fastq.gz,fastq,1701011300.0,34020226.0,GSM1357175 r1,0:50 1:0,A:453767169;C:401144167;G:392795706;T:453224665;N:79593,50,0,,,453767169,401144167,392795706,453224665,79593,SRX501294,SRS582366,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93437,,0.19214,,0.66884,,0.48995,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37969,SRR1205166,SRX501293,SRS582365,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 3hr 1,GSM1357174,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,cntl neo 3hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:negative|genotype:TgsqET20|experiment date:Apr2012,GSM1357174,GSM1357174: cntl neo 3hr 1; Danio rerio; RNA Seq,GSM1357174,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357174,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_3_1.fastq.gz,fastq,1228792200.0,24575844.0,GSM1357174 r1,0:50 1:0,A:328509222;C:288306723;G:283185002;T:328736353;N:54900,50,0,,,328509222,288306723,283185002,328736353,54900,SRX501293,SRS582365,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93269,,0.21003,,0.66592,,0.48875,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37970,SRR1205165,SRX501292,SRS582364,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 3,GSM1357173,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357173,GSM1357173: gfp neo 3hr 3; Danio rerio; RNA Seq,GSM1357173,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357173,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_3.fastq.gz,fastq,1406657700.0,28133154.0,GSM1357173 r1,0:50 1:0,A:379997165;C:326224852;G:320555458;T:379818406;N:61819,50,0,,,379997165,326224852,320555458,379818406,61819,SRX501292,SRS582364,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.9327,,0.3167,,0.70709,,0.48722,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37971,SRR1205164,SRX501291,SRS582363,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 2,GSM1357172,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357172,GSM1357172: gfp neo 3hr 2; Danio rerio; RNA Seq,GSM1357172,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357172,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_2.fastq.gz,fastq,1409177900.0,28183558.0,GSM1357172 r1,0:50 1:0,A:377366991;C:329654609;G:322942817;T:379147506;N:65977,50,0,,,377366991,329654609,322942817,379147506,65977,SRX501291,SRS582363,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.92559,,0.27573,,0.69968,,0.48668,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37972,SRR1205163,SRX501290,SRS582362,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 3hr 1,GSM1357171,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,gfp neo 3hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:3hr|gfp status:positive|genotype:TgsqET20|experiment date:Apr2012,GSM1357171,GSM1357171: gfp neo 3hr 1; Danio rerio; RNA Seq,GSM1357171,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357171,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_3_1.fastq.gz,fastq,1364255100.0,27285102.0,GSM1357171 r1,0:50 1:0,A:367031933;C:317262942;G:311363762;T:368536308;N:60155,50,0,,,367031933,317262942,311363762,368536308,60155,SRX501290,SRS582362,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93433,,0.34822,,0.70504,,0.49052,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37973,SRR1205162,SRX501289,SRS582361,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 3,GSM1357170,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357170,GSM1357170: gfp nt 1hr 3; Danio rerio; RNA Seq,GSM1357170,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357170,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_3.fastq.gz,fastq,2032585500.0,40651710.0,GSM1357170 r1,0:50 1:0,A:540423336;C:478257444;G:470055372;T:543729414;N:119934,50,0,,,540423336,478257444,470055372,543729414,119934,SRX501289,SRS582361,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93511,,0.2696,,0.70425,,0.49291,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37974,SRR1205161,SRX501288,SRS582360,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 2,GSM1357169,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357169,GSM1357169: gfp nt 1hr 2; Danio rerio; RNA Seq,GSM1357169,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357169,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_2.fastq.gz,fastq,1562346650.0,31246933.0,GSM1357169 r1,0:50 1:0,A:414164641;C:369142355;G:361974997;T:416978503;N:86154,50,0,,,414164641,369142355,361974997,416978503,86154,SRX501288,SRS582360,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93897,,0.31695,,0.70991,,0.50448,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37975,SRR1205160,SRX501287,SRS582359,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp nt 1hr 1,GSM1357168,,tissue:GFP positive cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp nt 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357168,GSM1357168: gfp nt 1hr 1; Danio rerio; RNA Seq,GSM1357168,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357168,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_nt_1_1.fastq.gz,fastq,1689050050.0,33781001.0,GSM1357168 r1,0:50 1:0,A:453271567;C:394505701;G:386090706;T:455068897;N:113179,50,0,,,453271567,394505701,386090706,455068897,113179,SRX501287,SRS582359,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93627,,0.28408,,0.70585,,0.48065,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37976,SRR1205159,SRX501286,SRS582358,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 3,GSM1357167,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357167,GSM1357167: gfp neo 1hr 3; Danio rerio; RNA Seq,GSM1357167,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357167,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_3.fastq.gz,fastq,1611919200.0,32238384.0,GSM1357167 r1,0:50 1:0,A:428150047;C:380113504;G:372605259;T:430955158;N:95232,50,0,,,428150047,380113504,372605259,430955158,95232,SRX501286,SRS582358,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94024,,0.31287,,0.71601,,0.50103,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37977,SRR1205158,SRX501285,SRS582357,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 2,GSM1357166,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357166,GSM1357166: gfp neo 1hr 2; Danio rerio; RNA Seq,GSM1357166,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357166,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_2.fastq.gz,fastq,1653679950.0,33073599.0,GSM1357166 r1,0:50 1:0,A:439492851;C:388625865;G:381772828;T:443698911;N:89495,50,0,,,439492851,388625865,381772828,443698911,89495,SRX501285,SRS582357,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94345,,0.38847,,0.7357,,0.50373,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37978,SRR1205157,SRX501284,SRS582356,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,gfp neo 1hr 1,GSM1357165,,tissue:GFP positive cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,gfp neo 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP positive cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:positive|genotype:TgsqET20|experiment date:Mar2012,GSM1357165,GSM1357165: gfp neo 1hr 1; Danio rerio; RNA Seq,GSM1357165,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357165,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,gfp_neo_1_1.fastq.gz,fastq,1873022200.0,37460444.0,GSM1357165 r1,0:50 1:0,A:501397145;C:438845045;G:428481612;T:504171995;N:126403,50,0,,,501397145,438845045,428481612,504171995,126403,SRX501284,SRS582356,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.933,,0.24769,,0.70591,,0.50587,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37979,SRR1205156,SRX501283,SRS582355,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 3,GSM1357164,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357164,GSM1357164: cntl nt 1hr 3; Danio rerio; RNA Seq,GSM1357164,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357164,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_3.fastq.gz,fastq,1523970250.0,30479405.0,GSM1357164 r1,0:50 1:0,A:404458518;C:360948466;G:353690676;T:404782977;N:89613,50,0,,,404458518,360948466,353690676,404782977,89613,SRX501283,SRS582355,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93995,,0.21232,,0.66772,,0.48499,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37980,SRR1205155,SRX501282,SRS582354,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 2,GSM1357163,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357163,GSM1357163: cntl nt 1hr 2; Danio rerio; RNA Seq,GSM1357163,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357163,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_2.fastq.gz,fastq,1649622150.0,32992443.0,GSM1357163 r1,0:50 1:0,A:434980357;C:392949654;G:385359402;T:436242531;N:90206,50,0,,,434980357,392949654,385359402,436242531,90206,SRX501282,SRS582354,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.94128,,0.24395,,0.67549,,0.50787,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37981,SRR1205154,SRX501281,SRS582353,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl nt 1hr 1,GSM1357162,,tissue:GFP negative cells from 5 dpf larvae|drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl nt 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:no drug|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357162,GSM1357162: cntl nt 1hr 1; Danio rerio; RNA Seq,GSM1357162,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357162,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_nt_1_1.fastq.gz,fastq,1953710600.0,39074212.0,GSM1357162 r1,0:50 1:0,A:518489677;C:462970545;G:452495723;T:519623507;N:131148,50,0,,,518489677,462970545,452495723,519623507,131148,SRX501281,SRS582353,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93818,,0.2175,,0.66229,,0.50468,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37982,SRR1205153,SRX501280,SRS582352,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 3,GSM1357161,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 3,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357161,GSM1357161: cntl neo 1hr 3; Danio rerio; RNA Seq,GSM1357161,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_3.fastq.gz,fastq,1934085200.0,38681704.0,GSM1357161 r1,0:50 1:0,A:513203802;C:458221455;G:449581302;T:512967391;N:111250,50,0,,,513203802,458221455,449581302,512967391,111250,SRX501280,SRS582352,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93811,,0.22613,,0.66671,,0.49681,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37983,SRR1205152,SRX501279,SRS582351,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 2,GSM1357160,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 2,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357160,GSM1357160: cntl neo 1hr 2; Danio rerio; RNA Seq,GSM1357160,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357160,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_2.fastq.gz,fastq,1836127900.0,36722558.0,GSM1357160 r1,0:50 1:0,A:485828745;C:436091545;G:426562682;T:487543575;N:101353,50,0,,,485828745,436091545,426562682,487543575,101353,SRX501279,SRS582351,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93856,,0.23223,,0.67154,,0.5021,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
37984,SRR1205151,SRX501278,SRS582350,SRP040561,PRJNA242641,Gene expression analysis of hair cell regeneration in the zebrafish lateral line,GSE56176,Transcriptome Analysis,Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However  non mammalian animals e.g. birds  amphibian and fish regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates  we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA Seq analyses on regenerating support cells purified by fluorescence activated cell sorting FACS. The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration  because these cells can be acutely killed by exposure to neomycin  post which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. TgsqET20 larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 dpf dpf TgsqET20 larvae at 1  3 and 5 hours post neomycin treatment  as well as from a non treated control. Overall design: Transgenic zebrafish TgsqET20 larvae at 5 dpf were exposed to neomycin  dissociated  and FACS sorted into GFP positive and GFP negative populations at xxx  3  and 5 hours following treatment  along with a mock treated 1 hr control. The experiment was performed in triplicate  for a total of 24 samples.,,pubmed:24706903,,cntl neo 1hr 1,GSM1357159,,tissue:GFP negative cells from 5 dpf larvae|drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,cntl neo 1hr 1,Data was processed with CASAVA version 1.8.2 Sequence reads in fastq format were mapped to danRer7using tophat 1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3. Genome build: danRer7 Supplementary files format and content: FPKM values per gene.,GFP negative cells from 5 dpf larvae,For neomycin treatment  5dpf larvae were treated for 30min with 300μM neomycin Fisher BioReagents diluted in 0.5X E2 medium  rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild type larvae at 48 hpf under fluorescent stereoscope.,drug:neomycin|time:1hr|gfp status:negative|genotype:TgsqET20|experiment date:Mar2012,GSM1357159,GSM1357159: cntl neo 1hr 1; Danio rerio; RNA Seq,GSM1357159,,1,Two hundred 5dpf untreated TgsqET20 control or neomycin treated TgsqET20 larvae were anesthetized  collected in a 2mL tube  dissociated with trypsin and filtered to remove un dissociated tissue. A two gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions see Materials and Methods of associated manuscript for detailed FACS protocol. Approximately 30 000 GFP  or GFP+ cells were used for total RNA extraction using Trizol Invitrogen following the manufacturer’s manual. Libraries for RNA sequencing were made with poly A selected mRNA using the Illumina TruSeq RNA library construction kit v2 Illumina. The resulting libraries were purified using Agencourt AMPure XP system Backman Coulter  then quantified using a Bioanalyzer or Qubit Fluorometer Life Technologies.,GEO Accession:GSM1357159,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP040561,,loader:latf load,cntl_neo_1_1.fastq.gz,fastq,1687481850.0,33749637.0,GSM1357159 r1,0:50 1:0,A:448529802;C:398804686;G:391019451;T:449013498;N:114413,50,0,,,448529802,398804686,391019451,449013498,114413,SRX501278,SRS582350,SRA149178,GEO,"Seidel, Genomics, Stowers Institute",1,0.93698,,0.21557,,0.66436,,0.49756,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2014-03-25,Multi-stage,Multi-stage,Undetermined,Undetermined
41422,SRR4423114,SRX2245298,SRS1745858,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,egg pools from three different mothers,,Egg pool Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Egg|sex:not applicable|tissue:eggs|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Egg pool,99 6,99 6,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,eggRID0099BC06LargeZF.fastq,fastq,4454090954.0,48098559.0,eggRID0099BC06LargeZF.fastq,0:92.60,A:1084275872;C:1151665265;G:1338679196;T:879470621;N:0,92,,,,1084275872,1151665265,1338679196,879470621,0,SRX2245298,SRS1745858,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.91346,,0.27222,,0.96694,,0.91118,,144,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Undetermined,Undetermined,Undetermined,Undetermined
48909,SRR7615221,SRX4479802,SRS3604791,SRP155604,PRJNA479418,Lariat intronic RNAs in the cytoplasm of vertebrate cells,PRJNA479418,Other,Introns are non coding DNA sequences interspersed among the coding sequences of genes. Shortly post transcription  the intronic sequences are spliced out of the primary RNA transcript as lariat RNAs circular molecules with a short tail. Most of these lariats are destroyed within minutes in the cell nucleus. We report here that many such intronic RNAs are  in fact  exported to the cytoplasm  where they remain as stable circular molecules. These cytoplasmic introns are derived from hundreds of different genes of widely different functions. We find them in cells of human  mouse  chicken  frog  and zebrafish. The widespread occurrence of so many stable lariat RNAs in the cytoplasm suggests that they play some as yet unexpected role in cell metabolism.,,,,,zebrafish eggs plusRNaseR,,strain:AB strain|dev stage:Germline|sex:female|tissue:Egg|treatment:n1|rna treatment:rRNA depletion and RNase R|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Zebrafish egg plus RNaseR,Zf pR,Zf pR,rRNA depletion ribozero fellowed by TruSeq Stranded Total RNA illumina,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP155604,,,150112_Zebrafish_egg_plusRNaseR_50bp.fastq,fastq,1453087900.0,29061758.0,150112 Zebrafish egg plusRNaseR 50bp.fastq,0:50,A:316388483;C:426462939;G:363020331;T:347178488;N:37659,50,,,,316388483,426462939,363020331,347178488,37659,SRX4479802,SRS3604791,SRA746415,Carnegie Institution for Science|Department of Embryology,Carnegie Institution for Science,1,0.83263,,0.31979,,0.81592,,0.51542,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,ribozero,bulk,unknown,unknown,,United States,2018-07-28,Undetermined,Undetermined,Undetermined,Undetermined
48910,SRR7615223,SRX4479800,SRS3604789,SRP155604,PRJNA479418,Lariat intronic RNAs in the cytoplasm of vertebrate cells,PRJNA479418,Other,Introns are non coding DNA sequences interspersed among the coding sequences of genes. Shortly post transcription  the intronic sequences are spliced out of the primary RNA transcript as lariat RNAs circular molecules with a short tail. Most of these lariats are destroyed within minutes in the cell nucleus. We report here that many such intronic RNAs are  in fact  exported to the cytoplasm  where they remain as stable circular molecules. These cytoplasmic introns are derived from hundreds of different genes of widely different functions. We find them in cells of human  mouse  chicken  frog  and zebrafish. The widespread occurrence of so many stable lariat RNAs in the cytoplasm suggests that they play some as yet unexpected role in cell metabolism.,,,,,zebrafish eggs minusRNaseR,,strain:AB strain|dev stage:Germline|sex:female|tissue:Egg|treatment:n1|rna treatment:rRNA depletion|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of Zebrafish egg minus RNaseR,Zf mR,Zf mR,rRNA depletion ribozero fellowed by TruSeq Stranded Total RNA illumina,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP155604,,,150112_Zebrafish_egg_minusRNaseR_50bp.fastq,fastq,2440809700.0,48816194.0,150112 Zebrafish egg minusRNaseR 50bp.fastq,0:50,A:588729472;C:623954878;G:556893764;T:671166713;N:64873,50,,,,588729472,623954878,556893764,671166713,64873,SRX4479800,SRS3604789,SRA746415,Carnegie Institution for Science|Department of Embryology,Carnegie Institution for Science,1,0.92096,,0.07705,,0.72861,,0.50081,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,ribozero,bulk,unknown,unknown,,United States,2018-07-28,Undetermined,Undetermined,Undetermined,Undetermined
50533,SRR8129704,SRX4950826,SRS3993016,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2,GSM3449965,,tissue:Fli:GFP  sorted  3 days  RNeasy sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNeasy sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449965,GSM3449965: RNeasy sorted 2; Danio rerio; RNA Seq,GSM3449965,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449965,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,Q_1.fastq.gz,fastq,1059463914.0,14029229.0,GSM3449965 r1,0:75.52 1:0,A:284634446;C:242976410;G:245781627;T:286026099;N:45332,75,0,,,284634446,242976410,245781627,286026099,45332,SRX4950826,SRS3993016,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.91903,,0.09754,,0.73537,,0.48738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50534,SRR8129703,SRX4950825,SRS3993017,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 1,GSM3449964,,tissue:Fli:GFP  sorted  3 days  RNAqueous  sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 1,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNAqueous  sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449964,GSM3449964: RNAqueous sorted 1; Danio rerio; RNA Seq,GSM3449964,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449964,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,A_1.fastq.gz,fastq,1477268521.0,19562904.0,GSM3449964 r1,0:75.51 1:0,A:399601730;C:333778207;G:337372866;T:406448608;N:67110,75,0,,,399601730,333778207,337372866,406448608,67110,SRX4950825,SRS3993017,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.90617,,0.09373,,0.74558,,0.49316,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
51017,SRR8435109,SRX5242689,SRS4245412,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 3,GSM3560348,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 3,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560348,GSM3560348: cldn15la GFP+ f Dex+ LREs 3; Danio rerio; RNA Seq,GSM3560348,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560348,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_3.fastq.gz,fastq,3319359633.0,65085483.0,GSM3560348 r1,0:51 1:0,A:939171958;C:728294535;G:735458210;T:914956028;N:1478902,51,0,,,939171958,728294535,735458210,914956028,1478902,SRX5242689,SRS4245412,SRA833636,GEO,Duke University,1,0.92838,,0.08491,,0.73507,,0.45124,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51018,SRR8435108,SRX5242688,SRS4245413,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 2,GSM3560347,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 2,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560347,GSM3560347: cldn15la GFP+ f Dex+ LREs 2; Danio rerio; RNA Seq,GSM3560347,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560347,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_2.fastq.gz,fastq,3886795782.0,76211682.0,GSM3560347 r1,0:51 1:0,A:1104818772;C:851405074;G:855078243;T:1073758670;N:1735023,51,0,,,1104818772,851405074,855078243,1073758670,1735023,SRX5242688,SRS4245413,SRA833636,GEO,Duke University,1,0.9367,,0.08433,,0.73565,,0.60818,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51019,SRR8435107,SRX5242687,SRS4245410,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ f Dex+ LREs 1,GSM3560346,,tissue:cldn15la GFP+ f Dex+ LREs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,cldn15la GFP+ f Dex+ LREs 1,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ f Dex+ LREs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs,GSM3560346,GSM3560346: cldn15la GFP+ f Dex+ LREs 1; Danio rerio; RNA Seq,GSM3560346,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560346,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,LRE_1.fastq.gz,fastq,3052804104.0,59858904.0,GSM3560346 r1,0:51 1:0,A:886286208;C:657679423;G:656279895;T:852223208;N:335370,51,0,,,886286208,657679423,656279895,852223208,335370,SRX5242687,SRS4245410,SRA833636,GEO,Duke University,1,0.92375,,0.09247,,0.77449,,0.67251,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51020,SRR8435106,SRX5242686,SRS4245411,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 3,GSM3560345,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 3,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560345,GSM3560345: cldn15la GFP+ IECs 3; Danio rerio; RNA Seq,GSM3560345,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560345,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_3.fastq.gz,fastq,3411376434.0,66889734.0,GSM3560345 r1,0:51 1:0,A:962628477;C:748798542;G:754301765;T:944119253;N:1528397,51,0,,,962628477,748798542,754301765,944119253,1528397,SRX5242686,SRS4245411,SRA833636,GEO,Duke University,1,0.92544,,0.11398,,0.71125,,0.50352,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51021,SRR8435105,SRX5242685,SRS4245408,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 2,GSM3560344,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 2,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560344,GSM3560344: cldn15la GFP+ IECs 2; Danio rerio; RNA Seq,GSM3560344,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560344,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_2.fastq.gz,fastq,4165555866.0,81677566.0,GSM3560344 r1,0:51 1:0,A:1164142809;C:924263682;G:930812689;T:1144479148;N:1857538,51,0,,,1164142809,924263682,930812689,1144479148,1857538,SRX5242685,SRS4245408,SRA833636,GEO,Duke University,1,0.92974,,0.09982,,0.7167,,0.5209,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
51022,SRR8435104,SRX5242684,SRS4245409,SRP178513,PRJNA514721,Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut,GSE124970,Transcriptome Analysis,The goal of this RNA seq experiment was to compare gene expression profiles of two different intestinal cell populations Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid intestine in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 dpf dpf TgBACcldn15la GFPpd1034 transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2  and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la GFP positive intestinal epithelial cells IECs and cldn15la GFP  Alexa Fluor 568 double positive lysosome rich enterocytes LREs were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples  with 3 replicates each.,,pubmed:31474562,,cldn15la GFP+ IECs 1,GSM3560343,,tissue:cldn15la GFP+ IECs|strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,cldn15la GFP+ IECs 1,HiSeq Control Software used for basecalling Sequenced reads were trimmed for adapter sequences and low quality reads using FASTQ Groomer and FASTQ Quality Trimmer  followed by alignment to the GRCz10 reference genome using HISAT2. The number of reads counted for each gene was calculated using HTSeq. Genome build: GRCz10 Supplementary files format and content: .tabular files containing HT seq counts for each gene in each sample.,cldn15la GFP+ IECs,Zebrafish larvae were gavaged with 1 2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,,strain:EK|genotype/variation:wild type|age:6 dpf type:cldn15la GFP positive intestinal epithelial cells IECs,GSM3560343,GSM3560343: cldn15la GFP+ IECs 1; Danio rerio; RNA Seq,GSM3560343,,1,At 6 dpf 24 hrs post gavage  zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence activated cell sorting FACS. Total RNA was prepared from each population using RNeasy Micro Plus Kit Qiagen. Quality control was evaluated by Qubit and 2100 Bioanalyzer. Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM3560343,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP178513,,,IEC_1.fastq.gz,fastq,3258191610.0,63886110.0,GSM3560343 r1,0:51 1:0,A:941514468;C:707367673;G:717548605;T:891005627;N:755237,51,0,,,941514468,707367673,717548605,891005627,755237,SRX5242684,SRS4245409,SRA833636,GEO,Duke University,1,0.91133,,0.12919,,0.76274,,0.60572,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-01-11,Larval,Larval,Undetermined,Undetermined
52210,SRR9021058,SRX5799154,SRS4730324,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 1,,replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 1 20190506 1,WT 1 20190506 1,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT1.1.fq,fastq,1094498950.0,21889979.0,WT1.1.fq,0:50,A:291195764;C:255539280;G:262638316;T:284737693;N:387897,50,,,,291195764,255539280,262638316,284737693,387897,SRX5799154,SRS4730324,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94195,,0.09713,,0.66689,,0.47749,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
52211,SRR9021059,SRX5799153,SRS4730323,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 2,,replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 2 20190506 2,WT 2 20190506 2,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT2.1.fq,fastq,1095133200.0,21902664.0,WT2.1.fq,0:50,A:290594757;C:255644044;G:259681140;T:288014102;N:1199157,50,,,,290594757,255644044,259681140,288014102,1199157,SRX5799153,SRS4730323,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.93368,,0.09166,,0.67085,,0.46523,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
52212,SRR9021060,SRX5799152,SRS4730322,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,WT 3,,replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,WT 3 20190506 3,WT 3 20190506 3,RNA seq of WT Diano rerio,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,WT3.1.fq,fastq,1096083900.0,21921678.0,WT3.1.fq,0:50,A:290332094;C:256993500;G:263043956;T:285349722;N:364628,50,,,,290332094,256993500,263043956,285349722,364628,SRX5799152,SRS4730322,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94147,,0.10157,,0.66135,,0.47301,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
52213,SRR9021061,SRX5799151,SRS4730320,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 1,,replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 1 20190506 1,gcgr 1 20190506 1,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr1.1.fq,fastq,1096307200.0,21926144.0,gcgr1.1.fq,0:50,A:288839446;C:258297625;G:264630675;T:284199738;N:339716,50,,,,288839446,258297625,264630675,284199738,339716,SRX5799151,SRS4730320,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94131,,0.09307,,0.67574,,0.46993,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
52214,SRR9021062,SRX5799150,SRS4730321,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 2,,replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 2 20190506 2,gcgr 2 20190506 2,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr2.1.fq,fastq,1094410100.0,21888202.0,gcgr2.1.fq,0:50,A:290062779;C:256358687;G:264488431;T:282812212;N:687991,50,,,,290062779,256358687,264488431,282812212,687991,SRX5799150,SRS4730321,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94074,,0.09337,,0.67633,,0.46861,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
52215,SRR9021063,SRX5799149,SRS4730319,SRP195685,PRJNA541367,Global transcriptomic analysis of zebrafish glucagon receptor mutant,PRJNA541367,Other,We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.,,,,,gcgr 3,,replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal,,,,,,,,,Diano rerio transcriptome,gcgr 3 20190506 3,gcgr 3 20190506 3,RNA seq of Diano rerio with gcgr mutant,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,BGISEQ,BGISEQ-500,,SRP195685,,loader:fastq load.py,gcgr3.1.fq,fastq,1094284800.0,21885696.0,gcgr3.1.fq,0:50,A:289313514;C:257096636;G:264011408;T:283143600;N:719642,50,,,,289313514,257096636,264011408,283143600,719642,SRX5799149,SRS4730319,SRA883435,Xiamen University|School of Pharmaceutical Sciences,Xiamen University,1,0.94222,,0.09557,,0.67521,,0.46664,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-18,Larval,Larval,Undetermined,Undetermined
60827,SRR12536650,SRX9026395,SRS7277845,SRP279118,PRJNA659812,Defects in the zonule in loxl1 knock out zebrafish,PRJNA659812,Other,Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.,,,,,3 larvae loxl1 / ,,strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:3|BioSampleModel:Model organism or animal,,,,,,,,,7dpf ko,loxl1 zebrafish3,loxl1 zebrafish3,materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP279118,,,larvae_ko_20190920NA_ATAGCGAC_S101_L001_R1_001.fastq.gz larvae_ko_20190920NA_ATAGCGAC_S101_L001_R2_001.fastq.gz,fastq fastq,8570236936.0,28378268.0,larvae ko 20190920NA ATAGCGAC S101 L001 R1 001.fastq.gz,0:151 1:151,A:2291363400;C:1985315062;G:2023225375;T:2269717794;N:615305,151,151,,,2291363400,1985315062,2023225375,2269717794,615305,SRX9026395,SRS7277845,SRA1118248,Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science,Eye and ENT Hospital of Fudan University,2,0.95641,0.95018,0.09997,0.0968,0.68436,0.68627,0.45419,0.45754,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-27,Larval,Larval,Undetermined,Undetermined
60828,SRR12536651,SRX9026394,SRS7277844,SRP279118,PRJNA659812,Defects in the zonule in loxl1 knock out zebrafish,PRJNA659812,Other,Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.,,,,,2 larvae loxl1+/ ,,strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:2|BioSampleModel:Model organism or animal,,,,,,,,,7dpf het,loxl1 zebrafish2,loxl1 zebrafish2,materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP279118,,,larvae_het_20190930N_CGGATTGC_S300_L003_R1_001.fastq.gz larvae_het_20190930N_CGGATTGC_S300_L003_R2_001.fastq.gz,fastq fastq,5856779318.0,19393309.0,larvae het 20190930N CGGATTGC S300 L003 R1 001.fastq.gz,0:151 1:151,A:1552921599;C:1369101147;G:1376867518;T:1557750473;N:138581,151,151,,,1552921599,1369101147,1376867518,1557750473,138581,SRX9026394,SRS7277844,SRA1118248,Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science,Eye and ENT Hospital of Fudan University,2,0.95845,0.95108,0.0757,0.07156,0.6551,0.65644,0.47472,0.47519,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-27,Larval,Larval,Undetermined,Undetermined
60829,SRR12536652,SRX9026393,SRS7277843,SRP279118,PRJNA659812,Defects in the zonule in loxl1 knock out zebrafish,PRJNA659812,Other,Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.,,,,,1 larvae wildtype,,strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:1|BioSampleModel:Model organism or animal,,,,,,,,,7dpf wt,loxl1 zebrafish1,loxl1 zebrafish1,materials and methods,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP279118,,,larvae_AB_20190930N_CGACACAC_S299_L003_R1_001.fastq.gz larvae_AB_20190930N_CGACACAC_S299_L003_R2_001.fastq.gz,fastq fastq,6190673236.0,20498918.0,larvae AB 20190930N CGACACAC S299 L003 R1 001.fastq.gz,0:151 1:151,A:1650586924;C:1439612857;G:1445758759;T:1654565514;N:149182,151,151,,,1650586924,1439612857,1445758759,1654565514,149182,SRX9026393,SRS7277843,SRA1118248,Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science,Eye and ENT Hospital of Fudan University,2,0.95643,0.95006,0.08333,0.07911,0.64747,0.649,0.47878,0.4805,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-27,Larval,Larval,Undetermined,Undetermined
66964,SRR16965143,SRX13156592,SRS11088496,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,1mix,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:10 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :mixture group,mix 1,mix 1,96hpf zebrafish larvae mixture group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,mix2_1_2.fq.gz,fastq,3313823250.0,22092155.0,mix2 1 2.fq.gz,0:0 1:150,A:895726357;C:763402657;G:745765587;T:908922686;N:5963,0,150,,,895726357,763402657,745765587,908922686,5963,SRX13156592,SRS11088496,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.93604,,0.10794,,0.65587,,0.47956,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66965,SRR16965144,SRX13156591,SRS11088495,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,3enf,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:9 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :enrofloxacin group,enf 3,enf 3,96hpf zebrafish larvae enrofloxacin group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,enf_3.fq.gz,fastq,3304972350.0,22033149.0,enf 3.fq.gz,0:150 1:0,A:899427202;C:745999066;G:759917309;T:899625137;N:3636,150,0,,,899427202,745999066,759917309,899625137,3636,SRX13156591,SRS11088495,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94353,,0.10795,,0.66212,,0.47773,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66967,SRR16965146,SRX13156589,SRS11088492,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,3car,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :carbendazim group,car 3,car 3,96hpf zebrafish larvae carbendazim group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,car_3_1.fq.gz,fastq,3335622150.0,22237481.0,car 3 1.fq.gz,0:150 1:0,A:853229671;C:807433601;G:820478265;T:854475092;N:5521,150,0,,,853229671,807433601,820478265,854475092,5521,SRX13156589,SRS11088492,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.96567,,0.03093,,0.70997,,0.47751,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66968,SRR16965147,SRX13156588,SRS11088494,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,1car,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :carbendazim group,car 1,car 1,96hpf zebrafish larvae carbendazim group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,car_1_1.fq.gz,fastq,3378056400.0,22520376.0,car 1 1.fq.gz,0:150 1:0,A:886009175;C:795203398;G:809447342;T:887390300;N:6185,150,0,,,886009175,795203398,809447342,887390300,6185,SRX13156588,SRS11088494,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.95701,,0.05956,,0.67836,,0.4884,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66969,SRR16965148,SRX13156587,SRS11088491,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,3con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :control group,con 3,con 3,96hpf zebrafish larvae control group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,con_3_2.fq.gz,fastq,3359054500.0,33590545.0,con 3 2.fq.gz,0:100 1:0,A:914533337;C:755914202;G:773676246;T:914930715;N:0,100,0,,,914533337,755914202,773676246,914930715,0,SRX13156587,SRS11088491,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.95076,,0.10478,,0.65646,,0.49594,,100,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66970,SRR16965149,SRX13156586,SRS11088489,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,3mix,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:12 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :mixture group,mix 3,mix 3,96hpf zebrafish larvae mixture group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,,mix2_3_1.fq.gz,fastq,3362094000.0,33620940.0,mix2 3 1.fq.gz,0:100 1:0,A:916124379;C:755910593;G:768246534;T:921812494;N:0,100,0,,,916124379,755910593,768246534,921812494,0,SRX13156586,SRS11088489,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94894,,0.10416,,0.65342,,0.49475,,100,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-17,Larval,Larval,Undetermined,Undetermined
66972,SRR16965151,SRX13156584,SRS11088488,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,2con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :control group,con 2,con 2,96hpf zebrafish larvae control group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,loader:fastq load.py,con_2_2.fq,fastq,3324287550.0,22161917.0,con 2 2.fq.gz,0:150,A:848766265;C:812477645;G:798995610;T:864040426;N:7604,150,,,,848766265,812477645,798995610,864040426,7604,SRX13156584,SRS11088488,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.95546,,0.03524,,0.70027,,0.48649,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-22,Larval,Larval,Undetermined,Undetermined
66973,SRR16965152,SRX13156583,SRS11088487,SRP346547,PRJNA780808,transcriptomics of carbendazim and enrofloxacin on zebrafish embryos,PRJNA780808,Other,reveal a interaction between ENF and CAR on metabolic regulation during development,,,,,1con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio :control group,con 1,con 1,96hpf zebrafish larvae control group,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346547,,loader:fastq load.py,con_1_1.fq,fastq,3330724500.0,22204830.0,con 1 1.fq.gz,0:150,A:896812508;C:762246067;G:774062043;T:897597946;N:5936,150,,,,896812508,762246067,774062043,897597946,5936,SRX13156583,SRS11088487,SRA1329868,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94926,,0.08711,,0.66789,,0.48628,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-22,Larval,Larval,Undetermined,Undetermined
66975,SRR16959539,SRX13151073,SRS11083379,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,2dim,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:8 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : dimethomorph group,dim 2,dim 2,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,dim_2_1.fq.gz,fastq,3344257500.0,22295050.0,dim 2 1.fq.gz,0:150 1:0,A:895700119;C:767415749;G:784994320;T:896143585;N:3727,150,0,,,895700119,767415749,784994320,896143585,3727,SRX13151073,SRS11083379,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.9497,,0.08418,,0.66352,,0.49341,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66976,SRR16959540,SRX13151072,SRS11083378,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,1dim,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:7 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : dimethomorph group,dim 1,dim 1,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,dim_1_1.fq.gz,fastq,3318812250.0,22125415.0,dim 1 1.fq.gz,0:150 1:0,A:908481293;C:742787936;G:755930542;T:911608821;N:3658,150,0,,,908481293,742787936,755930542,911608821,3658,SRX13151072,SRS11083378,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94211,,0.11824,,0.65344,,0.47716,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66977,SRR16959541,SRX13151071,SRS11083377,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,3dif,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : difenoconazole group,dif 3,dif 3,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,dif_3_1.fq.gz,fastq,3318453000.0,22123020.0,dif 3 1.fq.gz,0:150 1:0,A:893975607;C:758489621;G:772391705;T:893592335;N:3732,150,0,,,893975607,758489621,772391705,893592335,3732,SRX13151071,SRS11083377,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94838,,0.08393,,0.66543,,0.4818,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66978,SRR16959542,SRX13151070,SRS11083376,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,2dif,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:5 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : difenoconazole group,dif 2,dif 2,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,dif_2_2.fq.gz,fastq,3304972350.0,22033149.0,dif 2 2.fq.gz,0:0 1:150,A:890456734;C:764917766;G:744757536;T:904833787;N:6527,0,150,,,890456734,764917766,744757536,904833787,6527,SRX13151070,SRS11083376,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.93514,,0.107,,0.6633,,0.47599,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66979,SRR16959543,SRX13151069,SRS11083375,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,1dif,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : difenoconazole group,dif 1,dif 1,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,dif_1_1.fq.gz,fastq,3295443900.0,21969626.0,dif 1 1.fq.gz,0:150 1:0,A:887936493;C:751636494;G:765508757;T:890358629;N:3527,150,0,,,887936493,751636494,765508757,890358629,3527,SRX13151069,SRS11083375,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94623,,0.09138,,0.66478,,0.4828,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66980,SRR16959544,SRX13151068,SRS11083374,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,3+con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : control group,con 3,con 3,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,con_3_1.fq.gz,fastq,3306406800.0,22042712.0,con 3 1.fq.gz,0:150 1:0,A:872740236;C:773482184;G:788334419;T:871846539;N:3422,150,0,,,872740236,773482184,788334419,871846539,3422,SRX13151068,SRS11083374,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.95458,,0.06103,,0.67409,,0.48439,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66982,SRR16959546,SRX13151066,SRS11083372,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,2+con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : control group,con 2,con 2,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,con_2_2.fq.gz,fastq,3324287550.0,22161917.0,con 2 2.fq.gz,0:0 1:150,A:848766265;C:812477645;G:798995610;T:864040426;N:7604,0,150,,,848766265,812477645,798995610,864040426,7604,SRX13151066,SRS11083372,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.95548,,0.03524,,0.70021,,0.4867,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
66983,SRR16959547,SRX13151065,SRS11083371,SRP346418,PRJNA780940,transcriptomics of difenoconazole and dimethomorph on zebrafish embryos,PRJNA780940,Other,Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples  so the deleterious effects of combined exposure warrant detailed examination. In this study  the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate  deformity rate  lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development  and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L  respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes  cdk1  and cdc20  thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone.,,,,,1+con,,strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio : control group,con 1,con 1,The final library was amplified with phi29 to make DNA nanoballs DNB  with more than 300 copies of one molecular.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP346418,,,con_1_1.fq.gz,fastq,3330724500.0,22204830.0,con 1 1.fq.gz,0:150 1:0,A:896812508;C:762246067;G:774062043;T:897597946;N:5936,150,0,,,896812508,762246067,774062043,897597946,5936,SRX13151065,SRS11083371,SRA1330365,China Agricultural University|College of animal science and technology,China Agricultural University,1,0.94925,,0.08711,,0.66772,,0.48635,,150,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-11-16,Larval,Larval,Undetermined,Undetermined
67975,SRR17547553,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L001_R1_001.fastq.gz,fastq,493772580.0,5878245.0,GSM5800168 r1,0:84 1:0,A:128397756;C:115517535;G:120125116;T:129730356;N:1817,84,0,,,128397756,115517535,120125116,129730356,1817,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94974,,0.09483,,0.66448,,0.48897,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67976,SRR17547554,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L002_R1_001.fastq.gz,fastq,493766280.0,5878170.0,GSM5800168 r2,0:84 1:0,A:128477502;C:115522900;G:119992333;T:129772804;N:741,84,0,,,128477502,115522900,119992333,129772804,741,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.9505,,0.09356,,0.66523,,0.48634,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67977,SRR17547555,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L003_R1_001.fastq.gz,fastq,496976340.0,5916385.0,GSM5800168 r3,0:84 1:0,A:129349577;C:116134089;G:121098756;T:130391798;N:2120,84,0,,,129349577,116134089,121098756,130391798,2120,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94792,,0.09514,,0.66649,,0.50107,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67978,SRR17547556,SRX13717013,SRS11594777,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 4 [Sus stress 9],GSM5800168,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 4 [Sus stress 9],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800168,GSM5800168: Susceptible stressed 4 [Sus stress 9]; Danio rerio; RNA Seq,GSM5800168 r1,GSM5800168,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_9_S20_L004_R1_001.fastq.gz,fastq,487456956.0,5803059.0,GSM5800168 r4,0:84 1:0,A:126864938;C:113982481;G:118534988;T:128073199;N:1350,84,0,,,126864938,113982481,118534988,128073199,1350,SRX13717013,SRS11594777,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94956,,0.09471,,0.66511,,0.49469,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67979,SRR17547485,SRX13717012,SRS11594776,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 3 [Sus stress 8],GSM5800167,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 3 [Sus stress 8],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800167,GSM5800167: Susceptible stressed 3 [Sus stress 8]; Danio rerio; RNA Seq,GSM5800167 r1,GSM5800167,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_8_S19_L001_R1_001.fastq.gz,fastq,469949424.0,5594636.0,GSM5800167 r1,0:84 1:0,A:122207126;C:109956823;G:113902389;T:123881345;N:1741,84,0,,,122207126,109956823,113902389,123881345,1741,SRX13717012,SRS11594776,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94972,,0.09791,,0.6664,,0.49913,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67980,SRR17547486,SRX13717012,SRS11594776,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 3 [Sus stress 8],GSM5800167,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 3 [Sus stress 8],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800167,GSM5800167: Susceptible stressed 3 [Sus stress 8]; Danio rerio; RNA Seq,GSM5800167 r1,GSM5800167,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_8_S19_L002_R1_001.fastq.gz,fastq,470296260.0,5598765.0,GSM5800167 r2,0:84 1:0,A:122377372;C:110023805;G:113912095;T:123982329;N:659,84,0,,,122377372,110023805,113912095,123982329,659,SRX13717012,SRS11594776,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.95012,,0.09839,,0.66582,,0.49555,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67981,SRR17547487,SRX13717012,SRS11594776,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 3 [Sus stress 8],GSM5800167,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 3 [Sus stress 8],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800167,GSM5800167: Susceptible stressed 3 [Sus stress 8]; Danio rerio; RNA Seq,GSM5800167 r1,GSM5800167,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_8_S19_L003_R1_001.fastq.gz,fastq,472975524.0,5630661.0,GSM5800167 r3,0:84 1:0,A:123148854;C:110502275;G:114829173;T:124493162;N:2060,84,0,,,123148854,110502275,114829173,124493162,2060,SRX13717012,SRS11594776,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94829,,0.0973,,0.66979,,0.49994,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67982,SRR17547488,SRX13717012,SRS11594776,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 3 [Sus stress 8],GSM5800167,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 3 [Sus stress 8],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800167,GSM5800167: Susceptible stressed 3 [Sus stress 8]; Danio rerio; RNA Seq,GSM5800167 r1,GSM5800167,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_8_S19_L004_R1_001.fastq.gz,fastq,464153676.0,5525639.0,GSM5800167 r4,0:84 1:0,A:120810718;C:108548372;G:112463520;T:122329645;N:1421,84,0,,,120810718,108548372,112463520,122329645,1421,SRX13717012,SRS11594776,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94949,,0.09859,,0.66827,,0.49261,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined
67983,SRR17547489,SRX13717011,SRS11594775,SRP354402,PRJNA796216,Stress resilience is established during development and is regulated by complement factors,GSE193433,Transcriptome Analysis,Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently  others are susceptible to the same stressors. Most existing information regarding the factors regulating stress resilience in vertebrates is from specific areas of the brain from adult rodents or humans. In order to study resilience during development  we established a new paradigm to identify resilience in zebrafish larvae. Using this assay  we identified resilient and susceptible subsets of zebrafish larvae at 6 dpf and performed gene expression analysis on whole larvae. Overall design: Total RNA from resilient and susceptible groups was extracted either at basal conditions or 30 minutes following a 5 minute stress. 5 biological replicates 1 larva per sample were subjected to next generation sequencing.,,pubmed:36640352,,Susceptible stressed 2 [Sus stress 7],GSM5800166,,tissue:Susceptible larva|source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,Susceptible stressed 2 [Sus stress 7],Reads were trimmed using cutadapt DOI: 10.14806/ej.17.1.200 parameters:  a ADAPTER1  A ADAPTER2  a “A{10}”  a “T{10}” –times 2  q 20  m 25. Reads were mapped to genome /shareDB/genomes/Danio rerio/UCSC/danRer11/Star index/ using STAR DOI: 10.1093/bioinformatics/bts635 v2.4.2a parameters: –alignEndsType EndToEnd  –outFilterMismatchNoverLmax 0.05  –twopassMode Basic. Counting was done using STAR. Normalization of the counts and differential expression analysis was performed using DESeq2 DOI: 10.1186/s13059 014 0550 8 Genome build: danRer11 Supplementary files format and content: Raw counts  normalized measurements  fold change post Deseq2,Susceptible larva,Zebrafish larvae were differentiated into resilient and susceptible groups at 6 dpf. They were let to rest for a day  and at 7 dpf  single larvae were collected in Trizol either at basal conditions or 30 minutes following a stressful event.,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,Wildtype zebrafish larvae were grown in uncrowded densities till 6 dpf,source type:Whole larva|strain:AB|archetype:Susceptible|age:7 dpf,GSM5800166,GSM5800166: Susceptible stressed 2 [Sus stress 7]; Danio rerio; RNA Seq,GSM5800166 r1,GSM5800166,1,RNA was extracted by the basic Trizol chloroform phase separation method  precipitated with isopropanol  washed with 80% ethanol and resuspended in water. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP354402,,,Sus_stress_7_S18_L001_R1_001.fastq.gz,fastq,874086108.0,10405787.0,GSM5800166 r1,0:84 1:0,A:228386999;C:203987204;G:211004751;T:230704008;N:3146,84,0,,,228386999,203987204,211004751,230704008,3146,SRX13717011,SRS11594775,SRA1355607,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",1,0.94829,,0.10093,,0.66645,,0.48133,,84,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2022-01-11,Larval,Larval,Undetermined,Undetermined