run_metadata: 64972

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
64972	SRR14999365	SRX11311653	SRS9340851	SRP324442	PRJNA738523	Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag	GSE178343	Other	Here we describe successful implementation of CUT&RUN for profiling protein DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3 H3K27me3 H3K9me3 and RNA polymerase II during zebrafish gastrulation. Using this data we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development. Overall design: CUT&RUN in 6hpf zebrafish embryos for H3K27me3 H3K4me3 H3K9me3 and pol II. Experiments performed in duplicate with an IgG control.				C 2	C 2		strain:not collected\|isolate:Similar in size\|breed:AB wild type\|ecotype:Illumina sequencing\|age:4 months\|dev stage:adult\|sex:not collected\|tissue:Liver and brain\|biomaterial provider:CZRC\|replicate:replicate =C 2\|BioSampleModel:Model organism or animal									C 2	FRAS210007514 2r	FRAS210007514 2r	0g/L;h=96h;zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP324442			C_96h_2_1.fq.gz C_96h_2_2.fq.gz	fastq fastq	6348703200.0	21162344.0	C 96h 2 1.fq.gz	0:150 1:150	A:1700541402;C:1478742180;G:1481199683;T:1688070707;N:149228	150	150			1700541402	1478742180	1481199683	1688070707	149228	SRX11311653	SRS9340851	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.94135	0.94114	0.05775	0.0572	0.66101	0.66265	0.50778	0.50788	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		United States	2021-06-30	Adult	Adult	Multi-tissue	Multi-system