run_metadata: 70049

This data as json

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
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