{"database": "metadata", "table": "run_metadata", "rows": [[68650, "SRR18090812", "SRX14241857", "SRS12062491", "SRP360814", "PRJNA809026", "Competition for H2A.Z underlies the developmental impacts of repetitive element de repression", "GSE197131", "Transcriptome Analysis", "The histone variant H2A.Z is central to early embryonic development  determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci  we find that H2A.Z resides at a subset of evolutionarily young repetitive elements  including DNA transposons  LINEs  and LTRs  during early zebrafish development. Moreover  increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the repressive histone modification H3K9me3  and a moderate increase in chromatin accessibility. Notably however  de repression of repetitive elements also leads to a significant reduction in H2A.Z over non repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences  but remarkably  these impacts are mitigated by augmentation of total H2A.Z protein  via transgenic over expression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de repression of repetitive elements  that repetitive elements can function as a nuclear sink for epigenetic factors  and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes. Overall design: H2A.Z genomic profiling and gene expression in DMSO  5AzadC and TDCIPP treated zebrafish embryos at 6hpf and 12hpf were generated by next generation sequencing.", "parent bioproject:PRJNA680996", "pubmed:37938830", null, "WT 5AzadC 12hpf totalRNA Rep3", "GSM5909692", null, "tissue:zebrafish embryos|developmental stage:12hpf type|treatment:5AzadC|geo loc name:missing|collection date:missing", "WT 5AzadC 12hpf totalRNA Rep3", "Sequencing reads were mapped with STAR with default setting v2.7.2a Count tables were generated by featureCounts v2.0.3 in subread using GRCz11.102.gtf with paired end mode. Differentially expressed genes were identified using DESeq2 v1.22.2 in R/3.5.1 Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters:   normalizeUsing RPKM   binSize 10 Genome build: Zv11 Supplementary files format and content: bigWig files and txt files", "zebrafish embryos", "Newly fertilized eggs were collected immediately post spawning  and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza dC   or with 0.1% DMSO for control group.", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", "Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle", "developmental stage:12hpf type|treatment:5AzadC", "GSM5909692", "GSM5909692: WT 5AzadC 12hpf totalRNA Rep3; Danio rerio; RNA Seq", "GSM5909692 r1", "GSM5909692", "1", "Treated embryos were collected in Trizol at 12hpf  and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol  then aqueous layer were purified with Zymo Direct zol RNA Miniprep kit. Total RNA seq libraries were constructed.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP360814", null, "loader:fastq load.py", "WT_5AzadC_12hpf_totalRNA_Rep3_Clean_Data1.fq.gz WT_5AzadC_12hpf_totalRNA_Rep3_Clean_Data2.fq.gz", "fastq fastq", 8310943727.0, 29921343.0, "GSM5909692 r1", "0:138.91 1:138.85", "A:976992283;C:3148978077;G:3219797077;T:965069423;N:106867", 138, 138, null, null, 976992283, 3148978077, 3219797077, 965069423, 106867, "SRX14241857", "SRS12062491", "SRA1376914", "Biomedical Genetics, University of Rochester Medical Center", "Biomedical Genetics, University of Rochester Medical Center", 2, 0.98421, 0.9888, 0.04569, 0.04567, 0.91088, 0.91041, 0.96779, 0.96841, 142, 142, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-21", "Segmentation", "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": ["68650"], "units": {}, "query_ms": 9.778948995517567}