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 6,DRR315802,DRX305194,DRS231989,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample4,SAMD00400823,,sample name:rw147 2.5dpf wildtype rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,DRX305194,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,,,,10262353995.0,34151547.0,DRR315802,0:150.27 1:150.22,A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550,150,150,,,2735078560,2386126821,2433638250,2707202814,307550,DRX305194,DRS231989,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95231,0.95295,0.09229,0.08773,0.71819,0.72107,0.46746,0.46617,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 7,DRR315801,DRX305193,DRS231988,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample3,SAMD00400822,,sample name:rw147 2.5dpf wildtype rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,DRX305193,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,,,,11516368634.0,38355888.0,DRR315801,0:150.15 1:150.10,A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954,150,150,,,3080341643,2678048339,2713051368,3044449330,477954,DRX305193,DRS231988,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95353,0.95634,0.08909,0.08533,0.71374,0.71252,0.45986,0.46059,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 8,DRR315800,DRX305192,DRS231987,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample2,SAMD00400821,,sample name:rw147 2.5dpf wildtype rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,DRX305192,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,,,,8814057148.0,29367513.0,DRR315800,0:150.09 1:150.04,A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957,150,150,,,2350403211,2054073465,2083044327,2326181188,354957,DRX305192,DRS231987,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95287,0.95643,0.0891,0.08586,0.70309,0.70252,0.46384,0.46281,151,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 9,DRR315799,DRX305191,DRS231986,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample1,SAMD00400820,,sample name:rw147 2.5dpf wildtype rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,DRX305191,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,,,,10491955578.0,34900682.0,DRR315799,0:150.34 1:150.28,A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831,150,150,,,2796521111,2446218287,2483414564,2765477785,323831,DRX305191,DRS231986,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9539,0.95646,0.08185,0.07808,0.70025,0.70013,0.44713,0.44987,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 10,DRR315798,DRX305190,DRS231985,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample4,SAMD00400819,,sample name:rw147 2.5dpf Mutant rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,DRX305190,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,,,,9197802250.0,30604326.0,DRR315798,0:150.30 1:150.24,A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028,150,150,,,2468967963,2130949980,2158692262,2438931017,261028,DRX305190,DRS231985,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95159,0.95439,0.10146,0.09758,0.71995,0.71983,0.46519,0.46797,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 11,DRR315797,DRX305189,DRS231984,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample3,SAMD00400818,,sample name:rw147 2.5dpf Mutant rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,DRX305189,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,,,,10498982078.0,34931731.0,DRR315797,0:150.31 1:150.25,A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945,150,150,,,2804535103,2445295179,2478768789,2770066062,316945,DRX305189,DRS231984,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95448,0.95652,0.0939,0.0887,0.71796,0.71847,0.46335,0.46615,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 12,DRR315796,DRX305188,DRS231983,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample2,SAMD00400817,,sample name:rw147 2.5dpf Mutant rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,DRX305188,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,,,,9850145990.0,32782079.0,DRR315796,0:150.26 1:150.21,A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024,150,150,,,2636205537,2286508705,2319481100,2607600624,350024,DRX305188,DRS231983,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95193,0.95472,0.09722,0.09375,0.7138,0.71299,0.45542,0.45994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 13,DRR315795,DRX305187,DRS231982,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample1,SAMD00400816,,sample name:rw147 2.5dpf Mutant rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,DRX305187,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,,,,9542039835.0,31780260.0,DRR315795,0:150.15 1:150.10,A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225,150,150,,,2543384204,2224374632,2258183435,2515655339,442225,DRX305187,DRS231982,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9528,0.95591,0.08656,0.0828,0.70352,0.70331,0.45316,0.44914,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise 34487,SRR31790708,SRX27151927,SRS23606412,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5 we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a nitric oxide synthase arachidonate 5 lipoxygenase b immunity related GTPase family e1 sulfotransferase family 5A and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation inflammatory and immune response leucocyte mediated cytotoxicity peptidase activator activity protein folding and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega Madison WI USA based on the manufacturer's protocol. The RNA quality of each sample was evaluated with a bioanalyzer and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina USA yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 2,GSM8695646,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695646,GSM8695646: RNA zebrafish larvae treated PM2.5 rep 2; Danio rerio; RNA Seq,GSM8695646 r1,GSM8695646,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_2_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_2_R2.fq.gz,fastq fastq,6499686900.0,21665623.0,GSM8695646 r1,0:150 1:150,A:1738791948;C:1515807515;G:1516684626;T:1724651740;N:3751071,150,150,,,1738791948,1515807515,1516684626,1724651740,3751071,SRX27151927,SRS23606412,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined 34488,SRR31790709,SRX27151926,SRS23606411,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5 we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a nitric oxide synthase arachidonate 5 lipoxygenase b immunity related GTPase family e1 sulfotransferase family 5A and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation inflammatory and immune response leucocyte mediated cytotoxicity peptidase activator activity protein folding and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega Madison WI USA based on the manufacturer's protocol. The RNA quality of each sample was evaluated with a bioanalyzer and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina USA yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 1,GSM8695645,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 1,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695645,GSM8695645: RNA zebrafish larvae treated PM2.5 rep 1; Danio rerio; RNA Seq,GSM8695645 r1,GSM8695645,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_1_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_1_R2.fq.gz,fastq fastq,10116536700.0,33721789.0,GSM8695645 r1,0:150 1:150,A:2712593040;C:2357036246;G:2349793342;T:2687696916;N:9417156,150,150,,,2712593040,2357036246,2349793342,2687696916,9417156,SRX27151926,SRS23606411,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined 34489,SRR31790710,SRX27151925,SRS23606410,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5 we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a nitric oxide synthase arachidonate 5 lipoxygenase b immunity related GTPase family e1 sulfotransferase family 5A and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation inflammatory and immune response leucocyte mediated cytotoxicity peptidase activator activity protein folding and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega Madison WI USA based on the manufacturer's protocol. The RNA quality of each sample was evaluated with a bioanalyzer and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina USA yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae control rep 2,GSM8695644,,source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing,RNA zebrafish larvae control rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,tissue:larvea|treatment:control,GSM8695644,GSM8695644: RNA zebrafish larvae control rep 2; Danio rerio; RNA Seq,GSM8695644 r1,GSM8695644,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_control_rep_2_R1.fq.gz RNA_zebrafish_larvae_control_rep_2_R2.fq.gz,fastq fastq,6347285700.0,21157619.0,GSM8695644 r1,0:150 1:150,A:1687168204;C:1494146408;G:1490096893;T:1672074832;N:3799363,150,150,,,1687168204,1494146408,1490096893,1672074832,3799363,SRX27151925,SRS23606410,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined 34490,SRR31790711,SRX27151924,SRS23606409,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5 we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a nitric oxide synthase arachidonate 5 lipoxygenase b immunity related GTPase family e1 sulfotransferase family 5A and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation inflammatory and immune response leucocyte mediated cytotoxicity peptidase activator activity protein folding and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega Madison WI USA based on the manufacturer's protocol. The RNA quality of each sample was evaluated with a bioanalyzer and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina USA yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae control rep 1,GSM8695643,,source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing,RNA zebrafish larvae control rep 1,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,tissue:larvea|treatment:control,GSM8695643,GSM8695643: RNA zebrafish larvae control rep 1; Danio rerio; RNA Seq,GSM8695643 r1,GSM8695643,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab Erlangen Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_control_rep_1_R1.fq.gz RNA_zebrafish_larvae_control_rep_1_R2.fq.gz,fastq fastq,8152835100.0,27176117.0,GSM8695643 r1,0:150 1:150,A:2164487396;C:1922161762;G:1918935266;T:2142562884;N:4687792,150,150,,,2164487396,1922161762,1918935266,2142562884,4687792,SRX27151924,SRS23606409,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined 59089,SRR11590436,SRX8157791,SRS6519805,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,Low Fli1+ rep2,GSM4491074,,tissue:Low Fli1+|cell population:Low Fli1+|genotype:Tgfli1:EGFP,Low Fli1+ rep2,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,Low Fli1+,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:Low Fli1+|genotype:Tgfli1:EGFP,GSM4491074,GSM4491074: Low Fli1+ rep2; Danio rerio; RNA Seq,GSM4491074,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491074,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5758_GGCTAC_L005_R1_001.fastq.gz CI5758_GGCTAC_L005_R2_001.fastq.gz,fastq fastq,9251096400.0,46255482.0,GSM4491074 r1,0:100 1:100,A:1769289964;C:2789674423;G:2860116416;T:1825482073;N:6533524,100,100,,,1769289964,2789674423,2860116416,1825482073,6533524,SRX8157791,SRS6519805,SRA1068019,GEO,University of Edinburgh,2,0.90817,0.91357,0.12465,0.1278,0.77717,0.78376,0.75104,0.7256,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 59090,SRR11590435,SRX8157790,SRS6519799,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,Low Fli1+ rep1,GSM4491073,,tissue:Low Fli1+|cell population:Low Fli1+|genotype:Tgfli1:EGFP,Low Fli1+ rep1,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,Low Fli1+,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:Low Fli1+|genotype:Tgfli1:EGFP,GSM4491073,GSM4491073: Low Fli1+ rep1; Danio rerio; RNA Seq,GSM4491073,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491073,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5703_CAGATC_L005_R1_001.fastq.gz CI5703_CAGATC_L005_R2_001.fastq.gz,fastq fastq,6814746200.0,34073731.0,GSM4491073 r1,0:100 1:100,A:1332637473;C:2025204245;G:2079298693;T:1372597674;N:5008115,100,100,,,1332637473,2025204245,2079298693,1372597674,5008115,SRX8157790,SRS6519799,SRA1068019,GEO,University of Edinburgh,2,0.88252,0.88837,0.1449,0.1472,0.77839,0.78291,0.71852,0.68399,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 59091,SRR11590434,SRX8157789,SRS6519800,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,Fli1 rep2,GSM4491072,,tissue:Fli1 |cell population:Fli1 |genotype:Tgfli1:EGFP,Fli1 rep2,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,Fli1 ,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:Fli1 |genotype:Tgfli1:EGFP,GSM4491072,GSM4491072: Fli1 rep2; Danio rerio; RNA Seq,GSM4491072,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491072,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5757_TAGCTT_L005_R1_001.fastq.gz CI5757_TAGCTT_L005_R2_001.fastq.gz,fastq fastq,8455897000.0,42279485.0,GSM4491072 r1,0:100 1:100,A:1612223258;C:2555349390;G:2614157473;T:1667931765;N:6235114,100,100,,,1612223258,2555349390,2614157473,1667931765,6235114,SRX8157789,SRS6519800,SRA1068019,GEO,University of Edinburgh,2,0.94331,0.94696,0.11995,0.12207,0.76075,0.76796,0.74158,0.71821,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 59092,SRR11590433,SRX8157788,SRS6519797,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,Fli1 rep1,GSM4491071,,tissue:Fli1 |cell population:Fli1 |genotype:Tgfli1:EGFP,Fli1 rep1,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,Fli1 ,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:Fli1 |genotype:Tgfli1:EGFP,GSM4491071,GSM4491071: Fli1 rep1; Danio rerio; RNA Seq,GSM4491071,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491071,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5701_GCCAAT_L005_R1_001.fastq.gz CI5701_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,7474115600.0,37370578.0,GSM4491071 r1,0:100 1:100,A:1480688513;C:2199814780;G:2256979094;T:1531256742;N:5376471,100,100,,,1480688513,2199814780,2256979094,1531256742,5376471,SRX8157788,SRS6519797,SRA1068019,GEO,University of Edinburgh,2,0.93558,0.94034,0.13594,0.13917,0.75118,0.75684,0.66654,0.68344,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 59093,SRR11590438,SRX8157787,SRS6519798,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,High Fli1+ rep2,GSM4491076,,tissue:High Fli1+|cell population:High Fli1+|genotype:Tgfli1:EGFP,High Fli1+ rep2,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,High Fli1+,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:High Fli1+|genotype:Tgfli1:EGFP,GSM4491076,GSM4491076: High Fli1+ rep2; Danio rerio; RNA Seq,GSM4491076,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491076,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5759_CTTGTA_L005_R1_001.fastq.gz CI5759_CTTGTA_L005_R2_001.fastq.gz,fastq fastq,6877313200.0,34386566.0,GSM4491076 r1,0:100 1:100,A:1171923636;C:2222996793;G:2262044883;T:1215116923;N:5230965,100,100,,,1171923636,2222996793,2262044883,1215116923,5230965,SRX8157787,SRS6519798,SRA1068019,GEO,University of Edinburgh,2,0.95139,0.95705,0.08927,0.09017,0.81312,0.82004,0.77768,0.75585,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 59094,SRR11590437,SRX8157786,SRS6519796,SRP257942,PRJNA627467,Fli1+ cells transcriptional analysis reveals LMO2 PRDM16 axis in angiogenesis,GSE149152,Transcriptome Analysis,Different GFP+ cell population were isolated from Tgfli1:EGFP zebrafish embryos. Novel roles of epigenetic modifiers in endothelial differentiation were identified. Overall design: Each sample has been run in duplicate with 2 files per each run,,pubmed:34330825,,High Fli1+ rep1,GSM4491075,,tissue:High Fli1+|cell population:High Fli1+|genotype:Tgfli1:EGFP,High Fli1+ rep1,Illumina Illumina Hi Seq 2500 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to dr10 whole genome Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated. Genome build: danio rerio10 Supplementary files format and content: Text files with FPKM values for each sample were grouped in a single excel file,High Fli1+,,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,,cell population:High Fli1+|genotype:Tgfli1:EGFP,GSM4491075,GSM4491075: High Fli1+ rep1; Danio rerio; RNA Seq,GSM4491075,,1,100 ng of total RNA was subjected to library synthesis Total RNA was enriched for the Poly A mRNA and reverse transcribed to double stranded cDNA.,GEO Accession:GSM4491075,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP257942,,,CI5705_ACTTGA_L005_R1_001.fastq.gz CI5705_ACTTGA_L005_R2_001.fastq.gz,fastq fastq,8541050000.0,42705250.0,GSM4491075 r1,0:100 1:100,A:1667536155;C:2542273851;G:2600174460;T:1724878449;N:6187085,100,100,,,1667536155,2542273851,2600174460,1724878449,6187085,SRX8157786,SRS6519796,SRA1068019,GEO,University of Edinburgh,2,0.92757,0.93319,0.14438,0.14609,0.78867,0.79346,0.72736,0.71784,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2020-04-22,Undetermined,Embryo,Undetermined,Embryo Imprecise 70042,SRR19364727,SRX15423206,SRS13146622,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,BaP eggs 4 RNA seq,GSM6180938,,source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,BaP eggs 4 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,BaP eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,GSM6180938,GSM6180938: BaP eggs 4 RNA seq; Danio rerio; RNA Seq,GSM6180938 r1,GSM6180938,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP376709,,loader:fastq load.py,BaP_eggs_8_R1.fastq.gz BaP_eggs_8_R2.fastq.gz,fastq fastq,19115420100.0,63718067.0,GSM6180938 r1,0:150 1:150,A:4851825995;C:4609263506;G:4922433150;T:4730809159;N:1088290,150,150,,,4851825995,4609263506,4922433150,4730809159,1088290,SRX15423206,SRS13146622,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94488,0.93103,0.10568,0.10357,0.73748,0.73957,0.48933,0.48151,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70043,SRR19364732,SRX15423205,SRS13146621,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,BaP eggs 3 RNA seq,GSM6180937,,source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,BaP eggs 3 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,BaP eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,GSM6180937,GSM6180937: BaP eggs 3 RNA seq; Danio rerio; RNA Seq,GSM6180937 r1,GSM6180937,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP376709,,loader:fastq load.py,BaP_eggs_7_R1.fastq.gz BaP_eggs_7_R2.fastq.gz,fastq fastq,19465596300.0,64885321.0,GSM6180937 r1,0:150 1:150,A:4900471856;C:4741543326;G:5043578096;T:4778894378;N:1108644,150,150,,,4900471856,4741543326,5043578096,4778894378,1108644,SRX15423205,SRS13146621,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93506,0.92058,0.122,0.11917,0.74326,0.74474,0.56012,0.56276,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70044,SRR19364728,SRX15423204,SRS13146620,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,BaP eggs 2 RNA seq,GSM6180936,,source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,BaP eggs 2 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,BaP eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,GSM6180936,GSM6180936: BaP eggs 2 RNA seq; Danio rerio; RNA Seq,GSM6180936 r1,GSM6180936,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP376709,,loader:fastq load.py,BaP_eggs_6_R1.fastq.gz BaP_eggs_6_R2.fastq.gz,fastq fastq,26226106500.0,87420355.0,GSM6180936 r1,0:150 1:150,A:6626146699;C:6360908364;G:6776635828;T:6460933487;N:1482122,150,150,,,6626146699,6360908364,6776635828,6460933487,1482122,SRX15423204,SRS13146620,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94617,0.93149,0.11317,0.11079,0.74054,0.74263,0.55952,0.55897,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70045,SRR19364731,SRX15423203,SRS13146619,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,BaP eggs 1 RNA seq,GSM6180935,,source name:BaP eggs|strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,BaP eggs 1 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,BaP eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Benzo[a]Pyrene,GSM6180935,GSM6180935: BaP eggs 1 RNA seq; Danio rerio; RNA Seq,GSM6180935 r1,GSM6180935,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP376709,,loader:fastq load.py,BaP_eggs_5_R1.fastq.gz BaP_eggs_5_R2.fastq.gz,fastq fastq,18086447700.0,60288159.0,GSM6180935 r1,0:150 1:150,A:4571847785;C:4383836533;G:4677889533;T:4451843797;N:1030052,150,150,,,4571847785,4383836533,4677889533,4451843797,1030052,SRX15423203,SRS13146619,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.9432,0.92614,0.11892,0.11711,0.73815,0.74,0.54654,0.54731,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70046,SRR19364729,SRX15423202,SRS13146618,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,control eggs 4 RNA seq,GSM6180934,,source name:control eggs|strain:5D|tissue:Eggs|treatment:Control,control eggs 4 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,control eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Control,GSM6180934,GSM6180934: control eggs 4 RNA seq; Danio rerio; RNA Seq,GSM6180934 r1,GSM6180934,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP376709,,loader:fastq load.py,Control_eggs_4_R1.fastq.gz Control_eggs_4_R2.fastq.gz,fastq fastq,19391871000.0,64639570.0,GSM6180934 r1,0:150 1:150,A:4939089340;C:4665115719;G:4975360720;T:4811207801;N:1097420,150,150,,,4939089340,4665115719,4975360720,4811207801,1097420,SRX15423202,SRS13146618,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.90666,0.88778,0.11871,0.11531,0.74578,0.74795,0.53529,0.5334,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70047,SRR19364730,SRX15423201,SRS13146617,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,control eggs 3 RNA seq,GSM6180933,,source name:control eggs|strain:5D|tissue:Eggs|treatment:Control,control eggs 3 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,control eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Control,GSM6180933,GSM6180933: control eggs 3 RNA seq; Danio rerio; RNA Seq,GSM6180933 r1,GSM6180933,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP376709,,loader:fastq load.py,Control_eggs_3_R1.fastq.gz Control_eggs_3_R2.fastq.gz,fastq fastq,17489942700.0,58299809.0,GSM6180933 r1,0:150 1:150,A:4443405922;C:4213832030;G:4502075354;T:4329638793;N:990601,150,150,,,4443405922,4213832030,4502075354,4329638793,990601,SRX15423201,SRS13146617,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.9475,0.93055,0.10441,0.10172,0.74085,0.74343,0.56917,0.571,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70048,SRR19364733,SRX15423200,SRS13146616,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,control eggs 2 RNA seq,GSM6180932,,source name:control eggs|strain:5D|tissue:Eggs|treatment:Control,control eggs 2 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,control eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Control,GSM6180932,GSM6180932: control eggs 2 RNA seq; Danio rerio; RNA Seq,GSM6180932 r1,GSM6180932,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP376709,,loader:fastq load.py,Control_eggs_2_R1.fastq.gz Control_eggs_2_R2.fastq.gz,fastq fastq,19848063900.0,66160213.0,GSM6180932 r1,0:150 1:150,A:5033909827;C:4791850093;G:5120951365;T:4900231037;N:1121578,150,150,,,5033909827,4791850093,5120951365,4900231037,1121578,SRX15423200,SRS13146616,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94254,0.92598,0.11605,0.11324,0.74199,0.74442,0.56003,0.49676,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined 70049,SRR19364734,SRX15423199,SRS13146615,SRP376709,PRJNA841653,Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior Gene Expression and DNA Methylation,GSE203631,Other,Benzo[a]pyrene BaP a polycyclic aromatic hydrocarbon PAH is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents. Following a dietary preconceptional exposure to BaP in zebrafish the objective of this study was to compare parental sex dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs sperm and 10 hpf embryos. Adult wild type 5D zebrafish were fed 708 µg BaP/g diet measured at a rate of 1% body weight twice/day 14 µg BaP/g fish/day for 21 days. Fish were spawned using a crossover design and parental F0 behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hpf in F1 & F2 larvae and again when F1s were adult. Compared to controls there was no significant effect of BaP exposure on adult behavior in F0 but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior 96 hpf photomotor response assay was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex dependent molecular mechanisms BaP mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS respectively on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions DMRs and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes. Overall design: Sexually mature 120 dpf 5D strain of zebrafish were fed either acetone alone or BaP treated 25 µg/g fish equivalent to 1250 µg/g food respectively TetraMin® Tropical Flakes. Paired 2x2 zebrafish in five replicate tanks per treatment group N=5 replicate tanks for a total 20 fish/group were allowed to acclimate for a week while maintained at 25.5 28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure fish were fed 1% body weight twice daily of the corresponding dose of BaP treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21 a cross over breeding design was implemented to assess sex specific contributions into the following groups: control males x control females BaP females x control males BaP males x control females and BaP males x BaP females. On days 22 and 23 no longer being exposed eggs were collected to determine reproductive success. On day 24 females and day 25 males fish were euthanized and gonad liver and brain were collected biobanked for future analysis. Furthermore sperm or eggs from the BaP exposed and control fish along with 10 hpf embryos from each cross 4 crosses were collected for RNA seq and DNA methylation analysis.,,,,control eggs 1 RNA seq,GSM6180931,,source name:control eggs|strain:5D|tissue:Eggs|treatment:Control,control eggs 1 RNA seq,DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using Salmon RNAseq statistical analysis using DESeq2 Assembly: GRCz11 Supplementary files format and content: Text format RNAseq data files contains read counts ; bigWig DNA methylation calls of differentially methylated regions. DMRs.,control eggs,,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer’s instructions  RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer’s instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample.  DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing 5’ methyl cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform. ,,strain:5D|tissue:Eggs|treatment:Control,GSM6180931,GSM6180931: control eggs 1 RNA seq; Danio rerio; RNA Seq,GSM6180931 r1,GSM6180931,1,Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo Cat # D7005 following the manufacturer's instructions RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer's instructions. RNA Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs 150 bp paired end sequencing per sample. DNA methylation profiling Starting input genomic DNA 100 ng was digested with 30 units of MspI NEB. Fragments were ligated to pre annealed adapters containing five prime methyl cytosine instead of cytosine according to Illumina's specified guidelines. Adaptor ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™ 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning™ Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™ 5 Cat#: D4003 for sequencing on an Illumina platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP376709,,loader:fastq load.py,Control_eggs_1_R1.fastq.gz Control_eggs_1_R2.fastq.gz,fastq fastq,19334898300.0,64449661.0,GSM6180931 r1,0:150 1:150,A:4874809508;C:4709685650;G:5004647639;T:4744672338;N:1083165,150,150,,,4874809508,4709685650,5004647639,4744672338,1083165,SRX15423199,SRS13146615,SRA1425343,"Aluru Lab, Biology, Woods Hole Oceanographic Institution","Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93357,0.91807,0.10685,0.10558,0.73801,0.74065,0.5458,0.54625,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2022-05-23,Undetermined,Multi-stage,Undetermined,Undetermined