run_metadata: 68645

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
68645	SRR18090807	SRX14241862	SRS12062496	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		H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2	GSM5909697		tissue:zebrafish embryos\|developmental stage:12hpf overexpression\|treatment:5AzadC\|geo loc name:missing\|collection date:missing	H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2	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 overexpression\|treatment:5AzadC	GSM5909697	GSM5909697: H2A.ZmCherry 5AzadC 12hpf totalRNA Rep2; Danio rerio; RNA Seq	GSM5909697 r1	GSM5909697	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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP360814		loader:fastq load.py	H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep2_Clean_Data1.fq.gz H2A.ZmCherry_5AzadC_12hpf_totalRNA_Rep2_Clean_Data2.fq.gz	fastq fastq	8417838534.0	30315023.0	GSM5909697 r1	0:138.87 1:138.81	A:1056052986;C:3111397305;G:3219318758;T:1030963544;N:105941	138	138			1056052986	3111397305	3219318758	1030963544	105941	SRX14241862	SRS12062496	SRA1376914	Biomedical Genetics, University of Rochester Medical Center	Biomedical Genetics, University of Rochester Medical Center	2	0.97654	0.98322	0.05557	0.05458	0.88483	0.88434	0.95181	0.95236	142	142	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		United States	2022-02-21	Segmentation	Embryo	Embryo Imprecise	All anatomical structures