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
125,DRR189379,DRX179844,DRS200410,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 3,SAMD00182222,,sample name:Emx3     Larva body 3|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182222,DRX179844,Emx3 /  Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182222,,,,1759409208.0,48872478.0,DRR189379,0:36,A:401147348;C:424523813;G:426350919;T:507310828;N:76300,36,,,,401147348,424523813,426350919,507310828,76300,DRX179844,DRS200410,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90975,,0.11439,,0.66076,,0.47775,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
126,DRR189378,DRX179843,DRS200409,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 2,SAMD00182221,,sample name:Emx3     Larva body 2|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182221,DRX179843,Emx3 /  Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182221,,,,1318201020.0,36616695.0,DRR189378,0:36,A:297850068;C:316786585;G:323717530;T:379789606;N:57231,36,,,,297850068,316786585,323717530,379789606,57231,DRX179843,DRS200409,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.9116,,0.11269,,0.65837,,0.46733,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
127,DRR189377,DRX179842,DRS200408,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3  /  larval zebrafish 5dpf 1,SAMD00182220,,sample name:Emx3     Larva body 1|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182220,DRX179842,Emx3 /  Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182220,,,,812483964.0,22568999.0,DRR189377,0:36,A:185173338;C:197790160;G:197482964;T:232000884;N:36618,36,,,,185173338,197790160,197482964,232000884,36618,DRX179842,DRS200408,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91107,,0.1171,,0.65981,,0.47458,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
128,DRR189376,DRX179841,DRS200449,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 3,SAMD00182219,,sample name:WT Larva body 3|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182219,DRX179841,WT Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182219,,,,4030038144.0,111945504.0,DRR189376,0:36,A:943709984;C:971756680;G:977594500;T:1136798448;N:178532,36,,,,943709984,971756680,977594500,1136798448,178532,DRX179841,DRS200449,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89574,,0.12331,,0.65831,,0.48096,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
129,DRR189375,DRX179840,DRS200448,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 2,SAMD00182218,,sample name:WT Larva body 2|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182218,DRX179840,WT Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182218,,,,1991670804.0,55324189.0,DRR189375,0:36,A:454367176;C:479012055;G:488407231;T:569793674;N:90668,36,,,,454367176,479012055,488407231,569793674,90668,DRX179840,DRS200448,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90911,,0.12455,,0.65494,,0.47971,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
130,DRR189374,DRX179839,DRS200447,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 1,SAMD00182217,,sample name:WT Larva body 1|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182217,DRX179839,WT Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182217,,,,1018340100.0,28287225.0,DRR189374,0:36,A:233370050;C:244140659;G:247795084;T:292989542;N:44765,36,,,,233370050,244140659,247795084,292989542,44765,DRX179839,DRS200447,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91078,,0.12578,,0.6524,,0.48016,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
173,DRR075397,DRX069311,DRS075492,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of control fish 7dpf,Control body,SAMD00065411,,sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065411,DRX069311,Control body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065411,,,,2653100352.0,73697232.0,DRR075397,0:36,A:656791658;C:620507513;G:625038612;T:750671135;N:91434,36,,,,656791658,620507513,625038612,750671135,91434,DRX069311,DRS075492,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89666,,0.15749,,0.67048,,0.47755,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Trunk,Surface Structure
9170,ERR216332,ERX190997,ERS094086,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689285,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689285|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#6,4927108,Illumina sequencing of library 4927108  constructed from sample accession ERS094086 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence GCCAATGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#6.bam,bam,3849223200.0,25661488.0,SC RUN 7896 6#6,0:75 1:75,A:1052343872;C:867977827;G:867966925;T:1060514703;N:419873,75,75,,,1052343872,867977827,867966925,1060514703,419873,ERX190997,ERS094086,ERA182034,SC,Wellcome Sanger Institute,2,0.94843,0.9504,0.09374,0.09366,0.71421,0.71916,0.5306,0.52809,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9171,ERR216331,ERX190996,ERS094085,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689286,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1689286|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#5,4927107,Illumina sequencing of library 4927107  constructed from sample accession ERS094085 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ACAGTGGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#5.bam,bam,5957027700.0,39713518.0,SC RUN 7896 6#5,0:75 1:75,A:1634176455;C:1344899134;G:1345048404;T:1632256963;N:646744,75,75,,,1634176455,1344899134,1345048404,1632256963,646744,ERX190996,ERS094085,ERA182034,SC,Wellcome Sanger Institute,2,0.94169,0.94387,0.09489,0.09587,0.69406,0.69869,0.51459,0.51918,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9172,ERR216330,ERX190995,ERS094084,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689283,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689283|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#4,4927106,Illumina sequencing of library 4927106  constructed from sample accession ERS094084 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TGACCACT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#4.bam,bam,4130918700.0,27539458.0,SC RUN 7896 6#4,0:75 1:75,A:1129107864;C:933544249;G:934913323;T:1132901907;N:451357,75,75,,,1129107864,933544249,934913323,1132901907,451357,ERX190995,ERS094084,ERA182034,SC,Wellcome Sanger Institute,2,0.94225,0.94433,0.09272,0.09299,0.70043,0.70534,0.51333,0.52182,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9173,ERR216329,ERX190994,ERS094083,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689282,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689282|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#3,4927105,Illumina sequencing of library 4927105  constructed from sample accession ERS094083 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TTAGGCAT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#3.bam,bam,5102725800.0,34018172.0,SC RUN 7896 6#3,0:75 1:75,A:1400946711;C:1145033579;G:1143298888;T:1412890130;N:556492,75,75,,,1400946711,1145033579,1143298888,1412890130,556492,ERX190994,ERS094083,ERA182034,SC,Wellcome Sanger Institute,2,0.93688,0.93952,0.07363,0.07321,0.69645,0.70161,0.48708,0.48926,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9174,ERR216328,ERX190993,ERS094082,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689281,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T10:04:12Z|ENA LAST UPDATE:2018 03 08T15:36:11Z|External Id:SAMEA1689281|INSDC center name:SC|INSDC first public:2013 01 07T10:04:12Z|INSDC last update:2018 03 08T15:36:11Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#2,4927104,Illumina sequencing of library 4927104  constructed from sample accession ERS094082 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence CGATGTTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#2.bam,bam,4350577950.0,29003853.0,SC RUN 7896 6#2,0:75 1:75,A:1214100125;C:955724962;G:954429461;T:1225838270;N:485132,75,75,,,1214100125,955724962,954429461,1225838270,485132,ERX190993,ERS094082,ERA182034,SC,Wellcome Sanger Institute,2,0.92911,0.93026,0.0749,0.07514,0.69418,0.69775,0.48934,0.49,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9175,ERR216327,ERX190992,ERS094081,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689284,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689284|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#1,4927103,Illumina sequencing of library 4927103  constructed from sample accession ERS094081 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ATCACGTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#1.bam,bam,5063629350.0,33757529.0,SC RUN 7896 6#1,0:75 1:75,A:1416301768;C:1110273098;G:1105481234;T:1431015934;N:557316,75,75,,,1416301768,1110273098,1105481234,1431015934,557316,ERX190992,ERS094081,ERA182034,SC,Wellcome Sanger Institute,2,0.93508,0.93634,0.11212,0.11206,0.70009,0.70538,0.50126,0.49177,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
11148,ERR10034072,ERX9574476,ERS12562187,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 5,SAMEA110464159,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464159|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE25|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE25|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19178,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr25.1.fastq.gz S879Nr25.2.fastq.gz,fastq fastq,10120435126.0,50403985.0,ena RUN TAB 05 08 2022 14:25:08:835 19179,0:100.39 1:100.39,A:2679131890;C:2420708190;G:2483153503;T:2537307238;N:134305,100,100,,,2679131890,2420708190,2483153503,2537307238,134305,ERX9574476,ERS12562187,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96973,0.97106,0.04979,0.04949,0.71252,0.71654,0.4806,0.49338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11149,ERR10034071,ERX9574475,ERS12562186,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 4,SAMEA110464158,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464158|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE24|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE24|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19176,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr24.1.fastq.gz S879Nr24.2.fastq.gz,fastq fastq,7845661906.0,39121993.0,ena RUN TAB 05 08 2022 14:25:08:835 19177,0:100.27 1:100.27,A:2096079479;C:1862247618;G:1929220494;T:1958006859;N:107456,100,100,,,2096079479,1862247618,1929220494,1958006859,107456,ERX9574475,ERS12562186,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96989,0.96986,0.04901,0.04902,0.71599,0.72301,0.48965,0.48827,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11150,ERR10034070,ERX9574474,ERS12562185,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 3,SAMEA110464157,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464157|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE23|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE23|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19174,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr23.1.fastq.gz S879Nr23.2.fastq.gz,fastq fastq,8270390422.0,41338131.0,ena RUN TAB 05 08 2022 14:25:08:835 19175,0:100.03 1:100.03,A:2156060704;C:1998612686;G:2055201244;T:2060404840;N:110948,100,100,,,2156060704,1998612686,2055201244,2060404840,110948,ERX9574474,ERS12562185,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97085,0.97083,0.04232,0.04236,0.7219,0.72671,0.47325,0.4807,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11151,ERR10034069,ERX9574473,ERS12562184,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 2,SAMEA110464156,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464156|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE22|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE22|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19172,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr22.1.fastq.gz S879Nr22.2.fastq.gz,fastq fastq,10977356920.0,54380062.0,ena RUN TAB 05 08 2022 14:25:08:834 19173,0:100.93 1:100.93,A:2852856166;C:2671616791;G:2798184312;T:2654546853;N:152798,100,100,,,2852856166,2671616791,2798184312,2654546853,152798,ERX9574473,ERS12562184,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.9765,0.97629,0.03531,0.03529,0.72025,0.72705,0.47808,0.46326,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11152,ERR10034068,ERX9574472,ERS12562183,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Metamorphic tissue without xxx from Danio rerio,Drerio metamorphic 1,SAMEA110464155,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464155|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE21|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE21|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19170,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr21.1.fastq.gz S879Nr21.2.fastq.gz,fastq fastq,11346084502.0,56210802.0,ena RUN TAB 05 08 2022 14:25:08:834 19171,0:100.92 1:100.92,A:2950787998;C:2755514202;G:2902131288;T:2737495846;N:155168,100,100,,,2950787998,2755514202,2902131288,2737495846,155168,ERX9574472,ERS12562183,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.9732,0.97208,0.02959,0.02983,0.72322,0.73135,0.47796,0.47326,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Undetermined,Undetermined,Trunk,Surface Structure
11153,ERR10034052,ERX9574456,ERS12562167,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 5,SAMEA110464139,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464139|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE5|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE5|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:829 19138,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr5.1.fastq.gz S879Nr5.2.fastq.gz,fastq fastq,7308445864.0,36509997.0,ena RUN TAB 05 08 2022 14:25:08:829 19139,0:100.09 1:100.09,A:1934019972;C:1742739870;G:1803466955;T:1828120200;N:98867,100,100,,,1934019972,1742739870,1803466955,1828120200,98867,ERX9574456,ERS12562167,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96596,0.96653,0.05312,0.05284,0.71323,0.71873,0.49632,0.48138,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11154,ERR10034051,ERX9574455,ERS12562166,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 4,SAMEA110464138,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464138|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE4|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE4|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:822 19136,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr4.1.fastq.gz S879Nr4.2.fastq.gz,fastq fastq,8046902370.0,40206331.0,ena RUN TAB 05 08 2022 14:25:08:829 19137,0:100.07 1:100.07,A:2154247315;C:1901540683;G:1965167700;T:2025838764;N:107908,100,100,,,2154247315,1901540683,1965167700,2025838764,107908,ERX9574455,ERS12562166,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96507,0.96543,0.05345,0.0533,0.71553,0.72123,0.48553,0.49,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11155,ERR10034050,ERX9574454,ERS12562165,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 3,SAMEA110464137,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464137|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE3|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE3|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19134,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr3.1.fastq.gz S879Nr3.2.fastq.gz,fastq fastq,10897526786.0,54442757.0,ena RUN TAB 05 08 2022 14:25:08:821 19135,0:100.08 1:100.08,A:2902340346;C:2590905706;G:2655361716;T:2748771201;N:147817,100,100,,,2902340346,2590905706,2655361716,2748771201,147817,ERX9574454,ERS12562165,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.93244,0.93322,0.04311,0.04269,0.72452,0.72723,0.49726,0.4784,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11156,ERR10034049,ERX9574453,ERS12562164,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 2,SAMEA110464136,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464136|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE2|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE2|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19132,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr2.1.fastq.gz S879Nr2.2.fastq.gz,fastq fastq,8516273680.0,42589650.0,ena RUN TAB 05 08 2022 14:25:08:821 19133,0:99.98 1:99.98,A:2232300748;C:2055212367;G:2121115843;T:2107529926;N:114796,99,99,,,2232300748,2055212367,2121115843,2107529926,114796,ERX9574453,ERS12562164,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97117,0.97187,0.05876,0.05804,0.72115,0.72689,0.51447,0.50827,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11157,ERR10034048,ERX9574452,ERS12562163,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio  D. aesculapii  Danio aff. kyathit striped  also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 1,SAMEA110464135,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464135|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE1|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE1|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:820 19130,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr1.1.fastq.gz S879Nr1.2.fastq.gz,fastq fastq,5477863098.0,27332001.0,ena RUN TAB 05 08 2022 14:25:08:821 19131,0:100.21 1:100.21,A:1436230762;C:1320194529;G:1370010454;T:1351352868;N:74485,100,100,,,1436230762,1320194529,1370010454,1351352868,74485,ERX9574452,ERS12562163,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97196,0.97163,0.05932,0.05814,0.72723,0.73348,0.50582,0.51053,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
24600,SRR25475196,SRX21207464,SRS18464933,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],GSM7671235,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671235,GSM7671235: Zebrafish PrP BMD5/50 [PrP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671235 r1,GSM7671235,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_3_1.fq.gz PrP_BMD5_50_3_2.fq.gz,fastq fastq,5877585306.0,19462203.0,GSM7671235 r1,0:151 1:151,A:1673096549;C:1287336870;G:1399452621;T:1517513965;N:185301,151,151,,,1673096549,1287336870,1399452621,1517513965,185301,SRX21207464,SRS18464933,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94721,0.94392,0.10307,0.10285,0.71474,0.7209,0.44676,0.44767,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24601,SRR25475197,SRX21207464,SRS18464933,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],GSM7671235,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671235,GSM7671235: Zebrafish PrP BMD5/50 [PrP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671235 r1,GSM7671235,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_3_3.fq.gz PrP_BMD5_50_3_4.fq.gz,fastq fastq,2592008620.0,8582810.0,GSM7671235 r2,0:151 1:151,A:736893507;C:572181175;G:612346091;T:670582360;N:5487,151,151,,,736893507,572181175,612346091,670582360,5487,SRX21207464,SRS18464933,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94766,0.94372,0.10432,0.10439,0.71108,0.7193,0.4466,0.45067,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24602,SRR25475198,SRX21207463,SRS18464932,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 2],GSM7671234,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671234,GSM7671234: Zebrafish PrP BMD5/50 [PrP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671234 r1,GSM7671234,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_2_1.fq.gz PrP_BMD5_50_2_2.fq.gz,fastq fastq,6523053228.0,21599514.0,GSM7671234 r1,0:151 1:151,A:1881747155;C:1402382759;G:1625853412;T:1612862952;N:206950,151,151,,,1881747155,1402382759,1625853412,1612862952,206950,SRX21207463,SRS18464932,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94694,0.93482,0.08725,0.08666,0.70729,0.72423,0.44992,0.43992,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24603,SRR25475199,SRX21207462,SRS18464931,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],GSM7671233,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671233,GSM7671233: Zebrafish PrP BMD5/50 [PrP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671233 r1,GSM7671233,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_1_1.fq.gz PrP_BMD5_50_1_2.fq.gz,fastq fastq,2090436450.0,6921975.0,GSM7671233 r1,0:151 1:151,A:595082772;C:455110337;G:489835116;T:550342388;N:65837,151,151,,,595082772,455110337,489835116,550342388,65837,SRX21207462,SRS18464931,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93897,0.93808,0.1192,0.11852,0.71703,0.71938,0.46566,0.48323,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24604,SRR25475200,SRX21207462,SRS18464931,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],GSM7671233,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671233,GSM7671233: Zebrafish PrP BMD5/50 [PrP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671233 r1,GSM7671233,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_1_3.fq.gz PrP_BMD5_50_1_4.fq.gz,fastq fastq,4126091912.0,13662556.0,GSM7671233 r2,0:151 1:151,A:1171476389;C:902866887;G:958669795;T:1093069759;N:9082,151,151,,,1171476389,902866887,958669795,1093069759,9082,SRX21207462,SRS18464931,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93709,0.93594,0.1203,0.11941,0.71666,0.71924,0.47229,0.47483,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24605,SRR25475201,SRX21207461,SRS18464930,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 3],GSM7671232,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671232,GSM7671232: Zebrafish PrP BMD5/10 [PrP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671232 r1,GSM7671232,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_3_1.fq.gz PrP_BMD5_10_3_2.fq.gz,fastq fastq,6850831646.0,22684873.0,GSM7671232 r1,0:151 1:151,A:1937014178;C:1514493141;G:1623449869;T:1775656465;N:217993,151,151,,,1937014178,1514493141,1623449869,1775656465,217993,SRX21207461,SRS18464930,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94857,0.94727,0.09818,0.0981,0.70849,0.71364,0.44643,0.44849,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24606,SRR25475202,SRX21207460,SRS18464929,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 2],GSM7671231,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671231,GSM7671231: Zebrafish PrP BMD5/10 [PrP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671231 r1,GSM7671231,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_2_2.fq.gz PrP_BMD5_10_2_1.fq.gz,fastq fastq,6143720390.0,20343445.0,GSM7671231 r1,0:151 1:151,A:1724246127;C:1362285676;G:1457061100;T:1599935999;N:191488,151,151,,,1724246127,1362285676,1457061100,1599935999,191488,SRX21207460,SRS18464929,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9488,0.94766,0.094,0.09263,0.70905,0.71348,0.45157,0.43474,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24607,SRR25475203,SRX21207459,SRS18464928,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],GSM7671230,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671230,GSM7671230: Zebrafish PrP BMD5/10 [PrP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671230 r1,GSM7671230,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_1_1.fq.gz PrP_BMD5_10_1_2.fq.gz,fastq fastq,4178827454.0,13837177.0,GSM7671230 r1,0:151 1:151,A:1203579431;C:904927450;G:969023531;T:1101165327;N:131715,151,151,,,1203579431,904927450,969023531,1101165327,131715,SRX21207459,SRS18464928,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94274,0.83776,0.12469,0.10926,0.71752,0.73235,0.47225,0.46096,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24608,SRR25475204,SRX21207459,SRS18464928,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],GSM7671230,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671230,GSM7671230: Zebrafish PrP BMD5/10 [PrP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671230 r1,GSM7671230,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_1_4.fq.gz PrP_BMD5_10_1_3.fq.gz,fastq fastq,2952201906.0,9775503.0,GSM7671230 r2,0:151 1:151,A:846361785;C:642990303;G:682081110;T:780762283;N:6425,151,151,,,846361785,642990303,682081110,780762283,6425,SRX21207459,SRS18464928,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9411,0.86904,0.12259,0.11244,0.71392,0.72498,0.47116,0.47213,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24609,SRR25475205,SRX21207458,SRS18464927,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 3],GSM7671229,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671229,GSM7671229: Zebrafish PrP BMD5 [PrP BMD5 3]; Danio rerio; RNA Seq,GSM7671229 r1,GSM7671229,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_3_1.fq.gz PrP_BMD5_3_2.fq.gz,fastq fastq,2629615774.0,8707337.0,GSM7671229 r1,0:151 1:151,A:672958732;C:650029361;G:685902591;T:620641878;N:83212,151,151,,,672958732,650029361,685902591,620641878,83212,SRX21207458,SRS18464927,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.96303,0.96205,0.15116,0.14889,0.74101,0.74548,0.57303,0.57751,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24610,SRR25475206,SRX21207458,SRS18464927,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 3],GSM7671229,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671229,GSM7671229: Zebrafish PrP BMD5 [PrP BMD5 3]; Danio rerio; RNA Seq,GSM7671229 r1,GSM7671229,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_3_3.fq.gz PrP_BMD5_3_4.fq.gz,fastq fastq,3949175782.0,13076741.0,GSM7671229 r2,0:151 1:151,A:1009211118;C:979393371;G:1019201024;T:941361479;N:8790,151,151,,,1009211118,979393371,1019201024,941361479,8790,SRX21207458,SRS18464927,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.96187,0.96117,0.14636,0.14393,0.73813,0.74357,0.55833,0.54801,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24611,SRR25475207,SRX21207457,SRS18464926,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 2],GSM7671228,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671228,GSM7671228: Zebrafish PrP BMD5 [PrP BMD5 2]; Danio rerio; RNA Seq,GSM7671228 r1,GSM7671228,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_2_1.fq.gz PrP_BMD5_2_3.fq.gz,fastq fastq,3744054362.0,12397531.0,GSM7671228 r1,0:151 1:151,A:1046548811;C:825316142;G:923103248;T:948967256;N:118905,151,151,,,1046548811,825316142,923103248,948967256,118905,SRX21207457,SRS18464926,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9498,0.9466,0.09201,0.09131,0.70749,0.71506,0.44879,0.45356,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24612,SRR25475208,SRX21207457,SRS18464926,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 2],GSM7671228,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671228,GSM7671228: Zebrafish PrP BMD5 [PrP BMD5 2]; Danio rerio; RNA Seq,GSM7671228 r1,GSM7671228,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_2_4.fq.gz PrP_BMD5_2_2.fq.gz,fastq fastq,2834446066.0,9385583.0,GSM7671228 r2,0:151 1:151,A:793660024;C:632067365;G:686377801;T:722334752;N:6124,151,151,,,793660024,632067365,686377801,722334752,6124,SRX21207457,SRS18464926,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95049,0.94632,0.09253,0.09174,0.70818,0.71612,0.44666,0.45596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24613,SRR25475209,SRX21207456,SRS18464925,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 1],GSM7671227,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671227,GSM7671227: Zebrafish PrP BMD5 [PrP BMD5 1]; Danio rerio; RNA Seq,GSM7671227 r1,GSM7671227,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_1_1.fq.gz PrP_BMD5_1_2.fq.gz,fastq fastq,3340124530.0,11060015.0,GSM7671227 r1,0:151 1:151,A:957829723;C:716152911;G:809681516;T:856354060;N:106320,151,151,,,957829723,716152911,809681516,856354060,106320,SRX21207456,SRS18464925,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94378,0.93571,0.10991,0.11032,0.71206,0.72214,0.45578,0.44853,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24614,SRR25475210,SRX21207456,SRS18464925,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 1],GSM7671227,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671227,GSM7671227: Zebrafish PrP BMD5 [PrP BMD5 1]; Danio rerio; RNA Seq,GSM7671227 r1,GSM7671227,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_1_3.fq.gz PrP_BMD5_1_4.fq.gz,fastq fastq,2589508060.0,8574530.0,GSM7671227 r2,0:151 1:151,A:743364548;C:559167183;G:621696228;T:665273843;N:6258,151,151,,,743364548,559167183,621696228,665273843,6258,SRX21207456,SRS18464925,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94424,0.93574,0.10895,0.1074,0.70796,0.7189,0.45538,0.45171,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24615,SRR25475211,SRX21207455,SRS18464924,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 3],GSM7671226,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671226,GSM7671226: Zebrafish EtP BMD5/50 [EtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671226 r1,GSM7671226,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_3_1.fq.gz EtP_BMD5_50_3_2.fq.gz,fastq fastq,12326499346.0,40816223.0,GSM7671226 r1,0:151 1:151,A:3465072251;C:2766110070;G:2948834852;T:3146092010;N:390163,151,151,,,3465072251,2766110070,2948834852,3146092010,390163,SRX21207455,SRS18464924,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95355,0.95009,0.08714,0.08568,0.70782,0.71589,0.45241,0.44173,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24616,SRR25475212,SRX21207454,SRS18464923,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],GSM7671225,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671225,GSM7671225: Zebrafish EtP BMD5/50 [EtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671225 r1,GSM7671225,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_2_1.fq.gz EtP_BMD5_50_2_2.fq.gz,fastq fastq,5873726350.0,19449425.0,GSM7671225 r1,0:151 1:151,A:1639375920;C:1316625633;G:1408239211;T:1509300317;N:185269,151,151,,,1639375920,1316625633,1408239211,1509300317,185269,SRX21207454,SRS18464923,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95095,0.948,0.0908,0.09017,0.70721,0.71224,0.45389,0.44586,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24617,SRR25475213,SRX21207454,SRS18464923,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],GSM7671225,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671225,GSM7671225: Zebrafish EtP BMD5/50 [EtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671225 r1,GSM7671225,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_2_3.fq.gz EtP_BMD5_50_2_4.fq.gz,fastq fastq,2920857930.0,9671715.0,GSM7671225 r2,0:151 1:151,A:813299743;C:659443837;G:696023886;T:752084294;N:6170,151,151,,,813299743,659443837,696023886,752084294,6170,SRX21207454,SRS18464923,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95323,0.94979,0.08949,0.08869,0.70698,0.71352,0.45222,0.45353,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24618,SRR25475214,SRX21207453,SRS18464922,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],GSM7671224,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671224,GSM7671224: Zebrafish EtP BMD5/50 [EtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671224 r1,GSM7671224,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_1_1.fq.gz EtP_BMD5_50_1_2.fq.gz,fastq fastq,3025090814.0,10016857.0,GSM7671224 r1,0:151 1:151,A:843465525;C:670123195;G:725506632;T:785899023;N:96439,151,151,,,843465525,670123195,725506632,785899023,96439,SRX21207453,SRS18464922,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.83589,0.94217,0.09452,0.1077,0.72299,0.71587,0.46107,0.45633,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24619,SRR25475215,SRX21207453,SRS18464922,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],GSM7671224,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671224,GSM7671224: Zebrafish EtP BMD5/50 [EtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671224 r1,GSM7671224,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_1_3.fq.gz EtP_BMD5_50_1_4.fq.gz,fastq fastq,2444467124.0,8094262.0,GSM7671224 r2,0:151 1:151,A:679461384;C:546010997;G:581087164;T:637902414;N:5165,151,151,,,679461384,546010997,581087164,637902414,5165,SRX21207453,SRS18464922,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.87197,0.94213,0.1003,0.10863,0.71616,0.71317,0.45283,0.45457,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24620,SRR25475216,SRX21207452,SRS18464921,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 3],GSM7671223,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671223,GSM7671223: Zebrafish EtP BMD5/10 [EtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671223 r1,GSM7671223,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_3_1.fq.gz EtP_BMD5_10_3_2.fq.gz,fastq fastq,9653108974.0,31963937.0,GSM7671223 r1,0:151 1:151,A:2697568973;C:2165083953;G:2288959836;T:2501191246;N:304966,151,151,,,2697568973,2165083953,2288959836,2501191246,304966,SRX21207452,SRS18464921,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95172,0.95023,0.08652,0.0862,0.70619,0.71076,0.45447,0.45094,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24621,SRR25475217,SRX21207451,SRS18464920,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],GSM7671222,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671222,GSM7671222: Zebrafish EtP BMD5/10 [EtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671222 r1,GSM7671222,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_2_1.fq.gz EtP_BMD5_10_2_3.fq.gz,fastq fastq,5341647952.0,17687576.0,GSM7671222 r1,0:151 1:151,A:1430194079;C:1246082391;G:1309862164;T:1355339151;N:170167,151,151,,,1430194079,1246082391,1309862164,1355339151,170167,SRX21207451,SRS18464920,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95672,0.95646,0.09343,0.09169,0.715,0.71644,0.44995,0.46948,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24622,SRR25475218,SRX21207451,SRS18464920,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],GSM7671222,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671222,GSM7671222: Zebrafish EtP BMD5/10 [EtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671222 r1,GSM7671222,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_2_2.fq.gz EtP_BMD5_10_2_4.fq.gz,fastq fastq,3095850924.0,10251162.0,GSM7671222 r2,0:151 1:151,A:825080641;C:727003748;G:754816513;T:788943347;N:6675,151,151,,,825080641,727003748,754816513,788943347,6675,SRX21207451,SRS18464920,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95773,0.95746,0.09154,0.09045,0.71145,0.71256,0.46379,0.46536,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24623,SRR25475219,SRX21207450,SRS18464919,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],GSM7671221,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671221,GSM7671221: Zebrafish EtP BMD5/10 [EtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671221 r1,GSM7671221,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_1_1.fq.gz EtP_BMD5_10_1_2.fq.gz,fastq fastq,3224223272.0,10676236.0,GSM7671221 r1,0:151 1:151,A:898136457;C:705998538;G:782593577;T:837393065;N:101635,151,151,,,898136457,705998538,782593577,837393065,101635,SRX21207450,SRS18464919,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94431,0.94367,0.11343,0.11295,0.71238,0.71439,0.46018,0.45575,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24624,SRR25475220,SRX21207450,SRS18464919,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],GSM7671221,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671221,GSM7671221: Zebrafish EtP BMD5/10 [EtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671221 r1,GSM7671221,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_1_3.fq.gz EtP_BMD5_10_1_4.fq.gz,fastq fastq,2881317070.0,9540785.0,GSM7671221 r2,0:151 1:151,A:802691268;C:638869913;G:685114354;T:754635149;N:6386,151,151,,,802691268,638869913,685114354,754635149,6386,SRX21207450,SRS18464919,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94507,0.94452,0.11308,0.11253,0.70694,0.71054,0.45347,0.45385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24625,SRR25475221,SRX21207449,SRS18464918,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 3],GSM7671220,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671220,GSM7671220: Zebrafish EtP BMD5 [EtP BMD5 3]; Danio rerio; RNA Seq,GSM7671220 r1,GSM7671220,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_3_1.fq.gz EtP_BMD5_3_2.fq.gz,fastq fastq,6513209840.0,21566920.0,GSM7671220 r1,0:151 1:151,A:1838683121;C:1445463908;G:1536948771;T:1691910424;N:203616,151,151,,,1838683121,1445463908,1536948771,1691910424,203616,SRX21207449,SRS18464918,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94921,0.94751,0.09226,0.09115,0.70429,0.70907,0.45338,0.45104,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24626,SRR25475222,SRX21207448,SRS18464917,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 2],GSM7671219,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671219,GSM7671219: Zebrafish EtP BMD5 [EtP BMD5 2]; Danio rerio; RNA Seq,GSM7671219 r1,GSM7671219,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_2_1.fq.gz EtP_BMD5_2_2.fq.gz,fastq fastq,4443955368.0,14715084.0,GSM7671219 r1,0:151 1:151,A:1226532150;C:1002488064;G:1058104219;T:1156690900;N:140035,151,151,,,1226532150,1002488064,1058104219,1156690900,140035,SRX21207448,SRS18464917,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95173,0.95111,0.09256,0.09128,0.70469,0.7093,0.44316,0.44626,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24627,SRR25475223,SRX21207448,SRS18464917,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 2],GSM7671219,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671219,GSM7671219: Zebrafish EtP BMD5 [EtP BMD5 2]; Danio rerio; RNA Seq,GSM7671219 r1,GSM7671219,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_2_3.fq.gz EtP_BMD5_2_4.fq.gz,fastq fastq,3368297808.0,11153304.0,GSM7671219 r2,0:151 1:151,A:924217123;C:766145954;G:797666843;T:880260403;N:7485,151,151,,,924217123,766145954,797666843,880260403,7485,SRX21207448,SRS18464917,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95185,0.95089,0.09135,0.08974,0.70453,0.70692,0.44872,0.45596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24628,SRR25475224,SRX21207447,SRS18464916,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 1],GSM7671218,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671218,GSM7671218: Zebrafish EtP BMD5 [EtP BMD5 1]; Danio rerio; RNA Seq,GSM7671218 r1,GSM7671218,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_1_1.fq.gz EtP_BMD5_1_2.fq.gz,fastq fastq,2340650396.0,7750498.0,GSM7671218 r1,0:151 1:151,A:667132609;C:510116860;G:548591619;T:614735275;N:74033,151,151,,,667132609,510116860,548591619,614735275,74033,SRX21207447,SRS18464916,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94031,0.93918,0.11457,0.11486,0.71096,0.71482,0.46017,0.45386,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24629,SRR25475225,SRX21207447,SRS18464916,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 1],GSM7671218,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671218,GSM7671218: Zebrafish EtP BMD5 [EtP BMD5 1]; Danio rerio; RNA Seq,GSM7671218 r1,GSM7671218,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_1_3.fq.gz EtP_BMD5_1_4.fq.gz,fastq fastq,3046691364.0,10088382.0,GSM7671218 r2,0:151 1:151,A:865839573;C:668919023;G:709644830;T:802281652;N:6286,151,151,,,865839573,668919023,709644830,802281652,6286,SRX21207447,SRS18464916,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9416,0.93999,0.11428,0.11391,0.70816,0.71376,0.45095,0.45554,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24630,SRR25475226,SRX21207446,SRS18464915,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],GSM7671217,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671217,GSM7671217: Zebrafish MtP BMD5/50 [MtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671217 r1,GSM7671217,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_3_2.fq.gz MtP_BMD5_50_3_1.fq.gz,fastq fastq,3653327522.0,12097111.0,GSM7671217 r1,0:151 1:151,A:995366744;C:831318635;G:873618716;T:952906846;N:116581,151,151,,,995366744,831318635,873618716,952906846,116581,SRX21207446,SRS18464915,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95243,0.95252,0.09088,0.08971,0.7167,0.71711,0.45455,0.44644,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24631,SRR25475227,SRX21207446,SRS18464915,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],GSM7671217,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671217,GSM7671217: Zebrafish MtP BMD5/50 [MtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671217 r1,GSM7671217,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_3_3.fq.gz MtP_BMD5_50_3_4.fq.gz,fastq fastq,3423528474.0,11336187.0,GSM7671217 r2,0:151 1:151,A:928366145;C:784910903;G:813824790;T:896419194;N:7442,151,151,,,928366145,784910903,813824790,896419194,7442,SRX21207446,SRS18464915,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95366,0.9537,0.08926,0.08783,0.71423,0.71488,0.44252,0.44528,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24632,SRR25475228,SRX21207445,SRS18464914,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],GSM7671216,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671216,GSM7671216: Zebrafish MtP BMD5/50 [MtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671216 r1,GSM7671216,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_2_1.fq.gz MtP_BMD5_50_2_2.fq.gz,fastq fastq,4942474922.0,16365811.0,GSM7671216 r1,0:151 1:151,A:1353408937;C:1120658999;G:1177996657;T:1290253217;N:157112,151,151,,,1353408937,1120658999,1177996657,1290253217,157112,SRX21207445,SRS18464914,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95342,0.9531,0.08768,0.0872,0.71603,0.71741,0.4477,0.45194,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24633,SRR25475229,SRX21207445,SRS18464914,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],GSM7671216,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671216,GSM7671216: Zebrafish MtP BMD5/50 [MtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671216 r1,GSM7671216,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_2_4.fq.gz MtP_BMD5_50_2_3.fq.gz,fastq fastq,3002985622.0,9943661.0,GSM7671216 r2,0:151 1:151,A:819177253;C:685416613;G:712807034;T:785577695;N:7027,151,151,,,819177253,685416613,712807034,785577695,7027,SRX21207445,SRS18464914,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95358,0.95373,0.08626,0.08506,0.71539,0.71737,0.44723,0.45008,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24634,SRR25475230,SRX21207444,SRS18464913,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],GSM7671215,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671215,GSM7671215: Zebrafish MtP BMD5/50 [MtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671215 r1,GSM7671215,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_1_1.fq.gz MtP_BMD5_50_1_2.fq.gz,fastq fastq,5572679764.0,18452582.0,GSM7671215 r1,0:151 1:151,A:1572978393;C:1231505384;G:1304580144;T:1463439694;N:176149,151,151,,,1572978393,1231505384,1304580144,1463439694,176149,SRX21207444,SRS18464913,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94618,0.94569,0.10995,0.10957,0.71208,0.71577,0.44248,0.45317,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24635,SRR25475231,SRX21207444,SRS18464913,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],GSM7671215,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671215,GSM7671215: Zebrafish MtP BMD5/50 [MtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671215 r1,GSM7671215,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_1_3.fq.gz MtP_BMD5_50_1_4.fq.gz,fastq fastq,3433554572.0,11369386.0,GSM7671215 r2,0:151 1:151,A:966269363;C:763349843;G:801297479;T:902630496;N:7391,151,151,,,966269363,763349843,801297479,902630496,7391,SRX21207444,SRS18464913,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94553,0.94332,0.10986,0.10805,0.70989,0.71388,0.45838,0.45123,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24636,SRR25475232,SRX21207443,SRS18464912,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],GSM7671214,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671214,GSM7671214: Zebrafish MtP BMD5/10 [MtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671214 r1,GSM7671214,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_3_1.fq.gz MtP_BMD5_10_3_2.fq.gz,fastq fastq,5569270486.0,18441293.0,GSM7671214 r1,0:151 1:151,A:1574836056;C:1234020787;G:1290444481;T:1469794057;N:175105,151,151,,,1574836056,1234020787,1290444481,1469794057,175105,SRX21207443,SRS18464912,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95004,0.94806,0.10109,0.10024,0.71088,0.71415,0.45842,0.43735,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24637,SRR25475233,SRX21207443,SRS18464912,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],GSM7671214,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671214,GSM7671214: Zebrafish MtP BMD5/10 [MtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671214 r1,GSM7671214,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_3_3.fq.gz MtP_BMD5_10_3_4.fq.gz,fastq fastq,2514406700.0,8325850.0,GSM7671214 r2,0:151 1:151,A:708216865;C:560027758;G:582256307;T:663900270;N:5500,151,151,,,708216865,560027758,582256307,663900270,5500,SRX21207443,SRS18464912,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94944,0.94814,0.10054,0.10067,0.70751,0.71246,0.45622,0.44451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24638,SRR25475234,SRX21207442,SRS18464911,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],GSM7671213,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671213,GSM7671213: Zebrafish MtP BMD5/10 [MtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671213 r1,GSM7671213,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_2_1.fq.gz MtP_BMD5_10_2_2.fq.gz,fastq fastq,3506823396.0,11611998.0,GSM7671213 r1,0:151 1:151,A:982455627;C:781917114;G:848218674;T:894124856;N:107125,151,151,,,982455627,781917114,848218674,894124856,107125,SRX21207442,SRS18464911,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9504,0.94715,0.09519,0.09469,0.71147,0.718,0.44922,0.43458,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24639,SRR25475235,SRX21207442,SRS18464911,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],GSM7671213,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671213,GSM7671213: Zebrafish MtP BMD5/10 [MtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671213 r1,GSM7671213,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_2_3.fq.gz MtP_BMD5_10_2_4.fq.gz,fastq fastq,2523360094.0,8355497.0,GSM7671213 r2,0:151 1:151,A:705451559;C:567104395;G:605344307;T:645454842;N:4991,151,151,,,705451559,567104395,605344307,645454842,4991,SRX21207442,SRS18464911,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95062,0.94751,0.09472,0.094,0.71005,0.71666,0.45245,0.44889,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24640,SRR25475236,SRX21207441,SRS18464910,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],GSM7671212,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671212,GSM7671212: Zebrafish MtP BMD5/10 [MtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671212 r1,GSM7671212,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_1_1.fq.gz MtP_BMD5_10_1_2.fq.gz,fastq fastq,4528464330.0,14994915.0,GSM7671212 r1,0:151 1:151,A:1261030694;C:1015640347;G:1058184835;T:1193464002;N:144452,151,151,,,1261030694,1015640347,1058184835,1193464002,144452,SRX21207441,SRS18464910,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9473,0.94598,0.11708,0.11509,0.71364,0.71522,0.4646,0.46444,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24641,SRR25475237,SRX21207441,SRS18464910,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],GSM7671212,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671212,GSM7671212: Zebrafish MtP BMD5/10 [MtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671212 r1,GSM7671212,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_1_3.fq.gz MtP_BMD5_10_1_4.fq.gz,fastq fastq,2980367030.0,9868765.0,GSM7671212 r2,0:151 1:151,A:825558450;C:671536928;G:694866440;T:788398550;N:6662,151,151,,,825558450,671536928,694866440,788398550,6662,SRX21207441,SRS18464910,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94762,0.9469,0.11432,0.11281,0.71001,0.71297,0.46658,0.45541,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24642,SRR25475238,SRX21207440,SRS18464909,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 3],GSM7671211,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671211,GSM7671211: Zebrafish MtP BMD5 [MtP BMD5 3]; Danio rerio; RNA Seq,GSM7671211 r1,GSM7671211,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_3_1.fq.gz MtP_BMD5_3_2.fq.gz,fastq fastq,4936487470.0,16345985.0,GSM7671211 r1,0:151 1:151,A:1378752654;C:1113742094;G:1158863879;T:1284972892;N:155951,151,151,,,1378752654,1113742094,1158863879,1284972892,155951,SRX21207440,SRS18464909,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95301,0.95122,0.0955,0.0941,0.71208,0.71648,0.44704,0.44817,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24643,SRR25475239,SRX21207440,SRS18464909,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 3],GSM7671211,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671211,GSM7671211: Zebrafish MtP BMD5 [MtP BMD5 3]; Danio rerio; RNA Seq,GSM7671211 r1,GSM7671211,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_3_3.fq.gz MtP_BMD5_3_4.fq.gz,fastq fastq,3298411686.0,10921893.0,GSM7671211 r2,0:151 1:151,A:917164468;C:748498488;G:774036441;T:858705230;N:7059,151,151,,,917164468,748498488,774036441,858705230,7059,SRX21207440,SRS18464909,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95205,0.95054,0.09425,0.09329,0.71011,0.71455,0.44566,0.44912,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24644,SRR25475240,SRX21207439,SRS18464908,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 2],GSM7671210,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671210,GSM7671210: Zebrafish MtP BMD5 [MtP BMD5 2]; Danio rerio; RNA Seq,GSM7671210 r1,GSM7671210,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_2_1.fq.gz MtP_BMD5_2_2.fq.gz,fastq fastq,6227362008.0,20620404.0,GSM7671210 r1,0:151 1:151,A:1715937364;C:1386359386;G:1515578719;T:1609287962;N:198577,151,151,,,1715937364,1386359386,1515578719,1609287962,198577,SRX21207439,SRS18464908,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9491,0.94828,0.10169,0.10078,0.71399,0.71605,0.45429,0.454,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24645,SRR25475241,SRX21207438,SRS18464907,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 1],GSM7671209,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671209,GSM7671209: Zebrafish MtP BMD5 [MtP BMD5 1]; Danio rerio; RNA Seq,GSM7671209 r1,GSM7671209,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_1_1.fq.gz MtP_BMD5_1_4.fq.gz,fastq fastq,4052874428.0,13420114.0,GSM7671209 r1,0:151 1:151,A:1131227099;C:867529007;G:1014888508;T:1039101737;N:128077,151,151,,,1131227099,867529007,1014888508,1039101737,128077,SRX21207438,SRS18464907,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94427,0.94289,0.11676,0.11646,0.71587,0.72013,0.4544,0.45822,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24646,SRR25475242,SRX21207438,SRS18464907,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 1],GSM7671209,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671209,GSM7671209: Zebrafish MtP BMD5 [MtP BMD5 1]; Danio rerio; RNA Seq,GSM7671209 r1,GSM7671209,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_1_2.fq.gz MtP_BMD5_1_3.fq.gz,fastq fastq,3419102060.0,11321530.0,GSM7671209 r2,0:151 1:151,A:962312797;C:746662074;G:817866377;T:892253758;N:7054,151,151,,,962312797,746662074,817866377,892253758,7054,SRX21207438,SRS18464907,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94437,0.94159,0.11604,0.11533,0.7122,0.71697,0.45308,0.45718,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24647,SRR25475243,SRX21207437,SRS18464906,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 3],GSM7671208,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671208,GSM7671208: Zebrafish Control [C 3]; Danio rerio; RNA Seq,GSM7671208 r1,GSM7671208,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_3_1.fq.gz C_3_2.fq.gz,fastq fastq,5057829560.0,16747780.0,GSM7671208 r1,0:151 1:151,A:1402165693;C:1118939077;G:1238989668;T:1297578003;N:157119,151,151,,,1402165693,1118939077,1238989668,1297578003,157119,SRX21207437,SRS18464906,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95294,0.95134,0.09354,0.09252,0.71758,0.72255,0.44734,0.44399,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24648,SRR25475244,SRX21207437,SRS18464906,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 3],GSM7671208,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 3],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671208,GSM7671208: Zebrafish Control [C 3]; Danio rerio; RNA Seq,GSM7671208 r1,GSM7671208,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_3_3.fq.gz C_3_4.fq.gz,fastq fastq,2444105026.0,8093063.0,GSM7671208 r2,0:151 1:151,A:677519922;C:547933936;G:588011673;T:630634167;N:5328,151,151,,,677519922,547933936,588011673,630634167,5328,SRX21207437,SRS18464906,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95279,0.95095,0.09225,0.09186,0.71532,0.72021,0.44267,0.42467,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24649,SRR25475245,SRX21207436,SRS18464905,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 2],GSM7671207,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 2],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671207,GSM7671207: Zebrafish Control [C 2]; Danio rerio; RNA Seq,GSM7671207 r1,GSM7671207,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_2_1.fq.gz C_2_2.fq.gz,fastq fastq,6798305692.0,22510946.0,GSM7671207 r1,0:151 1:151,A:1815427330;C:1575068301;G:1689634001;T:1717960363;N:215697,151,151,,,1815427330,1575068301,1689634001,1717960363,215697,SRX21207436,SRS18464905,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95273,0.95222,0.10352,0.10219,0.71806,0.71952,0.468,0.47405,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24650,SRR25475246,SRX21207435,SRS18464904,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 1],GSM7671206,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671206,GSM7671206: Zebrafish Control [C 1]; Danio rerio; RNA Seq,GSM7671206 r1,GSM7671206,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_1_1.fq.gz C_1_2.fq.gz,fastq fastq,4775780888.0,15813844.0,GSM7671206 r1,0:151 1:151,A:1349640328;C:1033890598;G:1150153417;T:1241944276;N:152269,151,151,,,1349640328,1033890598,1150153417,1241944276,152269,SRX21207435,SRS18464904,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93975,0.93846,0.11061,0.11057,0.70796,0.7122,0.45018,0.4485,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24651,SRR25475247,SRX21207435,SRS18464904,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl   ethyl   and propyl  parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl  MtP  ethyl  EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5  embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0  M PoD/50  M PoD/10  and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens  as determined by M PoD values of 154.1  72.6  and 24.2 µM for MtP  EtP  and PrP  respectively. While exposure to EtP resulted in hyperactivity  no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal  transport  calcium ion binding  and metal binding. In contrast  exposure to MtP and PrP mainly disrupted the membrane and transmembrane  which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs  tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM  EtP 3.85 µM  and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products""  funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 1],GSM7671206,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 1],Filtered reads  quality >20 and length >50  were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM  TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671206,GSM7671206: Zebrafish Control [C 1]; Danio rerio; RNA Seq,GSM7671206 r1,GSM7671206,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc.  Cincinnati  OH  USA  and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_1_3.fq.gz C_1_4.fq.gz,fastq fastq,2235109248.0,7401024.0,GSM7671206 r2,0:151 1:151,A:630617292;C:490828084;G:527489424;T:586169387;N:5061,151,151,,,630617292,490828084,527489424,586169387,5061,SRX21207435,SRS18464904,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94126,0.94112,0.10981,0.11011,0.70485,0.70995,0.44139,0.45284,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24906,SRR25532497,SRX21261798,SRS18515093,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.42 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S10,S10,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK1_1.fq.gz CK1_2.fq.gz,fastq fastq,6650697900.0,22168993.0,CK1 1.fq.gz,0:150 1:150,A:1918460669;C:1420936092;G:1412569553;T:1898656995;N:74591,150,150,,,1918460669,1420936092,1412569553,1898656995,74591,SRX21261798,SRS18515093,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.91765,0.91694,0.15569,0.15461,0.70185,0.7027,0.47761,0.47369,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24907,SRR25532498,SRX21261797,SRS18515092,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.41 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S9,S9,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH3_2.fq.gz MBTH3_1.fq.gz,fastq fastq,6333332100.0,21111107.0,MBTH3 1.fq.gz,0:150 1:150,A:1755718187;C:1429192980;G:1420776066;T:1727550080;N:94787,150,150,,,1755718187,1429192980,1420776066,1727550080,94787,SRX21261797,SRS18515092,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93518,0.93355,0.11668,0.11602,0.67799,0.67817,0.47705,0.47875,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24908,SRR25532499,SRX21261796,SRS18515091,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.40 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S8,S8,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH2_1.fq.gz MBTH2_2.fq.gz,fastq fastq,6373733400.0,21245778.0,MBTH2 1.fq.gz,0:150 1:150,A:1775132718;C:1430955007;G:1424605018;T:1742942742;N:97915,150,150,,,1775132718,1430955007,1424605018,1742942742,97915,SRX21261796,SRS18515091,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93081,0.93016,0.12061,0.11947,0.68215,0.68172,0.47956,0.48186,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24909,SRR25532500,SRX21261795,SRS18515090,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.39 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S7,S7,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH1_1.fq.gz MBTH1_2.fq.gz,fastq fastq,6224052600.0,20746842.0,MBTH1 1.fq.gz,0:150 1:150,A:1753175301;C:1379045823;G:1371537072;T:1720226102;N:68302,150,150,,,1753175301,1379045823,1371537072,1720226102,68302,SRX21261795,SRS18515090,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9276,0.92379,0.13642,0.13482,0.68416,0.68479,0.47638,0.47581,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24910,SRR25532501,SRX21261794,SRS18515089,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.38 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S6,S6,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM3_2.fq.gz MBTM3_1.fq.gz,fastq fastq,6885667800.0,22952226.0,MBTM3 1.fq.gz,0:150 1:150,A:1936367424;C:1526831248;G:1520656271;T:1901736749;N:76108,150,150,,,1936367424,1526831248,1520656271,1901736749,76108,SRX21261794,SRS18515089,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92736,0.92516,0.12801,0.12693,0.68982,0.69063,0.47163,0.4612,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24911,SRR25532502,SRX21261793,SRS18515088,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.37 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S5,S5,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM2_1.fq.gz MBTM2_2.fq.gz,fastq fastq,6529427400.0,21764758.0,MBTM2 1.fq.gz,0:150 1:150,A:1808908277;C:1472638598;G:1467975655;T:1779801002;N:103868,150,150,,,1808908277,1472638598,1467975655,1779801002,103868,SRX21261793,SRS18515088,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9296,0.93217,0.11772,0.11735,0.68262,0.68331,0.4724,0.4721,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24912,SRR25532503,SRX21261792,SRS18515087,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.36 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S4,S4,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM1_2.fq.gz MBTM1_1.fq.gz,fastq fastq,6733924800.0,22446416.0,MBTM1 1.fq.gz,0:150 1:150,A:1847490053;C:1535661831;G:1528806965;T:1821868439;N:97512,150,150,,,1847490053,1535661831,1528806965,1821868439,97512,SRX21261792,SRS18515087,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93177,0.93448,0.11165,0.11192,0.67722,0.67823,0.47325,0.46912,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24913,SRR25532504,SRX21261791,SRS18515086,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.35 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S3,S3,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL3_1.fq.gz MBTL3_2.fq.gz,fastq fastq,9066238500.0,30220795.0,MBTL3 1.fq.gz,0:150 1:150,A:2629692873;C:1932648084;G:1927694770;T:2576111685;N:91088,150,150,,,2629692873,1932648084,1927694770,2576111685,91088,SRX21261791,SRS18515086,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93079,0.91809,0.1476,0.14446,0.69201,0.69258,0.47663,0.47687,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24914,SRR25532505,SRX21261790,SRS18515085,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.44 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S12,S12,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK3_1.fq.gz CK3_2.fq.gz,fastq fastq,6596041200.0,21986804.0,CK3 1.fq.gz,0:150 1:150,A:1886076947;C:1431757712;G:1423068767;T:1855067482;N:70292,150,150,,,1886076947,1431757712,1423068767,1855067482,70292,SRX21261790,SRS18515085,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92168,0.92147,0.14797,0.14768,0.68962,0.68935,0.47874,0.48307,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24915,SRR25532506,SRX21261789,SRS18515084,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.43 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S11,S11,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK2_1.fq.gz CK2_2.fq.gz,fastq fastq,6749651400.0,22498838.0,CK2 1.fq.gz,0:150 1:150,A:1934306700;C:1451979582;G:1445551014;T:1917740723;N:73381,150,150,,,1934306700,1451979582,1445551014,1917740723,73381,SRX21261789,SRS18515084,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92261,0.92062,0.15096,0.14969,0.69783,0.69702,0.48303,0.49016,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24916,SRR25532507,SRX21261788,SRS18515083,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.34 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S2,S2,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL2_1.fq.gz MBTL2_2.fq.gz,fastq fastq,6868354800.0,22894516.0,MBTL2 1.fq.gz,0:150 1:150,A:1956017484;C:1493585329;G:1486220640;T:1932456728;N:74619,150,150,,,1956017484,1493585329,1486220640,1932456728,74619,SRX21261788,SRS18515083,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92126,0.91908,0.14701,0.14525,0.69394,0.69363,0.47281,0.47636,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24917,SRR25532508,SRX21261787,SRS18515082,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.33 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S1,S1,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL1_1.fq.gz MBTL1_2.fq.gz,fastq fastq,6305127900.0,21017093.0,MBTL1 1.fq.gz,0:150 1:150,A:1797030982;C:1364002775;G:1357954929;T:1786051425;N:87789,150,150,,,1797030982,1364002775,1357954929,1786051425,87789,SRX21261787,SRS18515082,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92195,0.92138,0.14404,0.1433,0.69656,0.69623,0.47185,0.46936,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
25369,SRR25869114,SRX21590526,SRS18768099,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T7Ce,,strain:AB wild type|age:96 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56809|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:7|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep3|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T7Ce S85,T7Ce S85,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T7Ce_S85_L003_R1_001.fastq.gz T7Ce_S85_L003_R2_001.fastq.gz,fastq fastq,4023236400.0,13410788.0,T7Ce S85 L003 R1 001.fastq.gz,0:150 1:150,A:1064722362;C:898468046;G:1026541856;T:1033441788;N:62348,150,150,,,1064722362,898468046,1026541856,1033441788,62348,SRX21590526,SRS18768099,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.63998,0.64782,0.1145,0.11833,0.72476,0.72366,0.51386,0.50933,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25370,SRR25869115,SRX21590525,SRS18768098,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T7Cd,,strain:AB wild type|age:96 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56808|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:7|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T7Cd S9,T7Cd S9,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T7Cd_S9_L003_R1_001.fastq.gz T7Cd_S9_L003_R2_001.fastq.gz,fastq fastq,5594836800.0,18649456.0,T7Cd S9 L003 R1 001.fastq.gz,0:150 1:150,A:1466668075;C:1268623063;G:1444679585;T:1414780182;N:85895,150,150,,,1466668075,1268623063,1444679585,1414780182,85895,SRX21590525,SRS18768098,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.6489,0.65814,0.10603,0.1096,0.72332,0.72259,0.51745,0.51597,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25371,SRR25869116,SRX21590524,SRS18768097,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T7Cc,,strain:AB wild type|age:96 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56807|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:7|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep1|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T7Cc S117,T7Cc S117,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T7Cc_S117_L003_R1_001.fastq.gz T7Cc_S117_L003_R2_001.fastq.gz,fastq fastq,5560971900.0,18536573.0,T7Cc S117 L003 R1 001.fastq.gz,0:150 1:150,A:1487669019;C:1227367015;G:1414625121;T:1431224819;N:85926,150,150,,,1487669019,1227367015,1414625121,1431224819,85926,SRX21590524,SRS18768097,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.63573,0.6453,0.11688,0.12088,0.72997,0.72902,0.51338,0.51387,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25372,SRR25869117,SRX21590523,SRS18768096,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T6Ce,,strain:AB wild type|age:48 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56806|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:6|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep3|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T6Ce S8,T6Ce S8,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T6Ce_S8_L003_R1_001.fastq.gz T6Ce_S8_L003_R2_001.fastq.gz,fastq fastq,4874754000.0,16249180.0,T6Ce S8 L003 R1 001.fastq.gz,0:150 1:150,A:1274050261;C:1103676303;G:1253372135;T:1243579950;N:75351,150,150,,,1274050261,1103676303,1253372135,1243579950,75351,SRX21590523,SRS18768096,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.63046,0.63966,0.07875,0.08075,0.71681,0.71549,0.47414,0.46325,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25373,SRR25869118,SRX21590522,SRS18768094,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T6Cd,,strain:AB wild type|age:48 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56805|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:6|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T6Cd S84,T6Cd S84,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T6Cd_S84_L003_R1_001.fastq.gz T6Cd_S84_L003_R2_001.fastq.gz,fastq fastq,4927384500.0,16424615.0,T6Cd S84 L003 R1 001.fastq.gz,0:150 1:150,A:1280134661;C:1104306525;G:1315380512;T:1227487382;N:75420,150,150,,,1280134661,1104306525,1315380512,1227487382,75420,SRX21590522,SRS18768094,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.58432,0.58907,0.07948,0.08138,0.72685,0.72683,0.49019,0.49519,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25374,SRR25869119,SRX21590521,SRS18768095,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T6Cc,,strain:AB wild type|age:48 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56804|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:6|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep1|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T6Cc S116,T6Cc S116,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T6Cc_S116_L003_R1_001.fastq.gz T6Cc_S116_L003_R2_001.fastq.gz,fastq fastq,4331403900.0,14438013.0,T6Cc S116 L003 R1 001.fastq.gz,0:150 1:150,A:1130928068;C:974224521;G:1128883853;T:1097300164;N:67294,150,150,,,1130928068,974224521,1128883853,1097300164,67294,SRX21590521,SRS18768095,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.63494,0.64261,0.09364,0.0961,0.72165,0.72056,0.49488,0.48947,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25375,SRR25869120,SRX21590520,SRS18768093,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T5Ce,,strain:AB wild type|age:24 120hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56803|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:5|dose:350.59|dose units:ug/L|treatment:PC transcr Chlorpyrifos CAS 2921 88 2|replicate ID:rep3|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo positive control Chlorpyrifos CAS 2921 88 2,T5Ce S115,T5Ce S115,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T5Ce_S115_L003_R1_001.fastq.gz T5Ce_S115_L003_R2_001.fastq.gz,fastq fastq,3631059600.0,12103532.0,T5Ce S115 L003 R1 001.fastq.gz,0:150 1:150,A:950373132;C:821009152;G:934794612;T:924826460;N:56244,150,150,,,950373132,821009152,934794612,924826460,56244,SRX21590520,SRS18768093,SRA1703741,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.64403,0.653,0.08469,0.08696,0.71303,0.71234,0.47952,0.48386,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Larval,Larval,Trunk,Surface Structure
25376,SRR25868914,SRX21590491,SRS18768063,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ad1,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56229|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:1687.3254831396318|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep1|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ad1 S259,T1Ad1 S259,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ad1_S259_L003_R1_001.fastq.gz T1Ad1_S259_L003_R2_001.fastq.gz,fastq fastq,7819723500.0,26065745.0,T1Ad1 S259 L003 R1 001.fastq.gz,0:150 1:150,A:2031599001;C:1759639807;G:2105335746;T:1923080206;N:68740,150,150,,,2031599001,1759639807,2105335746,1923080206,68740,SRX21590491,SRS18768063,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.59547,0.59971,0.05855,0.05976,0.74332,0.74477,0.48103,0.48162,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure
25377,SRR25868915,SRX21590490,SRS18768064,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ac5,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56228|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:6461.39165470093|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep5|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ac5 S5,T1Ac5 S5,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ac5_S5_L001_R1_001.fastq.gz T1Ac5_S5_L001_R2_001.fastq.gz,fastq fastq,7625048100.0,25416827.0,T1Ac5 S5 L001 R1 001.fastq.gz,0:150 1:150,A:1966966252;C:1726081062;G:2022524018;T:1909426914;N:49854,150,150,,,1966966252,1726081062,2022524018,1909426914,49854,SRX21590490,SRS18768064,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.59676,0.60268,0.06216,0.0642,0.74174,0.74113,0.47678,0.47717,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure
25378,SRR25868916,SRX21590489,SRS18768062,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ac4,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56227|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:6461.39165470093|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep4|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ac4 S383,T1Ac4 S383,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ac4_S383_L004_R1_001.fastq.gz T1Ac4_S383_L004_R2_001.fastq.gz,fastq fastq,6653231400.0,22177438.0,T1Ac4 S383 L004 R1 001.fastq.gz,0:150 1:150,A:1736107768;C:1497492478;G:1749793425;T:1669780748;N:56981,150,150,,,1736107768,1497492478,1749793425,1669780748,56981,SRX21590489,SRS18768062,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.6438,0.64822,0.06467,0.06566,0.73742,0.73807,0.47559,0.47987,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure
25379,SRR25868917,SRX21590488,SRS18768061,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ac3,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56226|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:6461.39165470093|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep3|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ac3 S132,T1Ac3 S132,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ac3_S132_L002_R1_001.fastq.gz T1Ac3_S132_L002_R2_001.fastq.gz,fastq fastq,4826356500.0,16087855.0,T1Ac3 S132 L002 R1 001.fastq.gz,0:150 1:150,A:1255196359;C:1087160424;G:1291949396;T:1192013773;N:36548,150,150,,,1255196359,1087160424,1291949396,1192013773,36548,SRX21590488,SRS18768061,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.63006,0.63488,0.06653,0.06719,0.74235,0.74207,0.47463,0.47853,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure
25380,SRR25868918,SRX21590487,SRS18768060,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ac2,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56225|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:6461.39165470093|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ac2 S4,T1Ac2 S4,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ac2_S4_L001_R1_001.fastq.gz T1Ac2_S4_L001_R2_001.fastq.gz,fastq fastq,5236125600.0,17453752.0,T1Ac2 S4 L001 R1 001.fastq.gz,0:150 1:150,A:1364663796;C:1155880460;G:1404167486;T:1311305290;N:108568,150,150,,,1364663796,1155880460,1404167486,1311305290,108568,SRX21590487,SRS18768060,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.57127,0.5764,0.05133,0.05264,0.74815,0.74789,0.46551,0.46517,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure
25381,SRR25868919,SRX21590486,SRS18768057,SRP457982,PRJNA1011844,Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds,PRJNA1011844,Other,The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.,,,,,T1Ac1,,strain:AB wild type|age:6 24hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 56224|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:1|dose:6461.39165470093|dose units:ug/L|treatment:PFOA CAS 45285 51 6|replicate ID:rep1|repeat sample:No|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6,T1Ac1 S258,T1Ac1 S258,At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457982,,,T1Ac1_S258_L003_R1_001.fastq.gz T1Ac1_S258_L003_R2_001.fastq.gz,fastq fastq,5556495600.0,18521652.0,T1Ac1 S258 L003 R1 001.fastq.gz,0:150 1:150,A:1456422234;C:1242170020;G:1458160272;T:1399693066;N:50008,150,150,,,1456422234,1242170020,1458160272,1399693066,50008,SRX21590486,SRS18768057,SRA1703738,U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division,U.S. Environmental Protection Agency,2,0.60445,0.61015,0.06801,0.06934,0.74363,0.74318,0.46687,0.46545,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,lexogen,bulk,unknown,unknown,,United States,2023-09-01,Pharyngula,Embryo,Trunk,Surface Structure