{"database": "metadata", "table": "run_metadata", "rows": [[65857, "SRR15657169", "SRX11954172", "SRS9963994", "SRP334492", "PRJNA758398", "Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]", "GSE182945", "Transcriptome Analysis", "Here  we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system  even the Cu2+ concentration is at 10 \u00b5g/L  the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS  retina  and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance  respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding  suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control  0.078 \u00b5M 5 \u00b5g/L  and 0.156 \u00b5M 10 \u00b5g/L Cu for over 21 days  with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly  50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 \u00b5M group; 0.156 \u00b5M group at 24 hpf and 96 hpf  respectively  and lysed by Trizol reagent Ambion  Life Technologies for RNA extraction and RNA sequencing RNA Seq.", "parent bioproject:PRJNA758396", null, null, "embryo Control 24hpf", "GSM5543524", null, "tissue:embryo  Control 24hpf|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "embryo Control 24hpf", "Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample", "embryo  Control 24hpf", "50 60 embryos F1 from each group", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "embryos F1 cultured in normal water environment", "cell type:embryos at 24hpf hours post  fertilization|treatment:embryos whose parents were exposed to normal water environment F0 fish|genotype:wild type zebrafish AB at 3 month F0 fish", "GSM5543524", "GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq", "GSM5543524", null, "1", "RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute", "GEO Accession:GSM5543524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP334492", null, null, "Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz", "fastq fastq", 6911559200.0, 69115592.0, "GSM5543524 r1", "0:100 1:100", "A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486", 100, 100, null, null, 1858569189, 1592355971, 1564572369, 1895593185, 468486, "SRX11954172", "SRS9963994", "SRA1284991", "GEO", "college of informatics, Huazhong Agricultural University", 1, 0.93745, null, 0.09795, null, 0.69059, null, 0.48209, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Multi-stage", "Multi-stage", "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": ["65857"], "units": {}, "query_ms": 13.31849900452653}