metadata: run_metadata: 12 rows where technology = "bulk" and tissue_curation

12 rows where technology = "bulk" and tissue_curation_coarse = "Undetermined"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34487	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	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	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	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
70042	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 …		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	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 …		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	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 …		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	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 …		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	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 …		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	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 …		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	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 …		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	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 …		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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;