{"database": "metadata", "table": "run_metadata", "rows": [[70032, "SRR19364717", "SRX15423216", "SRS13146632", "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 \u00b5g BaP/g diet measured at a rate of 1% body weight twice/day 14 \u00b5g 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 \u00b5g/g fish equivalent to 1250 \u00b5g/g food  respectively TetraMin\u00ae 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\u00b0C 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.", null, null, null, "Cf.Bm.10hpf  2 RNA seq", "GSM6180948", null, "source name:Cf.Bm.10hpf|strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "Cf.Bm.10hpf  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.", "Cf.Bm.10hpf", null, "Both RNA and DNA were extracted using a Quick DNA/RNA Miniprep Plus Kit Zymo  Cat # D7005 following the manufacturer\u2019s instructions\u00a0 RNAseq libraries were prepared using the Zymo Seq RiboFree Total RNA Library Prep Kit Cat # R3000 according to the manufacturer\u2019s 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.\u00a0 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\u2019 methyl cytosine instead of cytosine according to Illumina\u2019s specified guidelines. Adaptor ligated fragments \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.\u00a0", null, "strain:5D|tissue:10hpf embryos|treatment:Control female x BaP male", "GSM6180948", "GSM6180948: Cf.Bm.10hpf  2 RNA seq; Danio rerio; RNA Seq", "GSM6180948 r1", "GSM6180948", "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 \u226550 bp in size were recovered using the DNA Clean & Concentrator\u2122 5 Cat#: D4003. The fragments were then bisulfite treated using the EZ DNA Methylation Lightning\u2122 Kit Cat#: D5030. Preparative scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator\u2122 5 Cat#: D4003 for sequencing on an Illumina platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP376709", null, "loader:fastq load.py", "CfBm_10_hpf_18_R1.fastq.gz CfBm_10_hpf_18_R2.fastq.gz", "fastq fastq", 19820526900.0, 66068423.0, "GSM6180948 r1", "0:150 1:150", "A:4972408439;C:4835381551;G:5174213471;T:4837395455;N:1127984", 150, 150, null, null, 4972408439, 4835381551, 5174213471, 4837395455, 1127984, "SRX15423216", "SRS13146632", "SRA1425343", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.95061, 0.93663, 0.1414, 0.13768, 0.7696, 0.77264, 0.62446, 0.62332, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-05-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["70032"], "units": {}, "query_ms": 6.9185309985186905}