run_metadata: 64975

This data as json

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64975	SRR14999368	SRX11311650	SRS9340848	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.				H 2	H 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 =H 2\|BioSampleModel:Model organism or animal									H 2	FRAS210007516 2r	FRAS210007516 2r	2.0g/L;h=96h;zebrafish			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP324442			H_96h_2_1.fq.gz H_96h_2_2.fq.gz	fastq fastq	6161230800.0	20537436.0	H 96h 2 1.fq.gz	0:150 1:150	A:1637006263;C:1449880253;G:1451565756;T:1622634286;N:144242	150	150			1637006263	1449880253	1451565756	1622634286	144242	SRX11311650	SRS9340848	SRA1252645	Shandong Normal University\|School of geography and environment	Genetics, University of Goergia	2	0.93477	0.93452	0.02553	0.02539	0.72395	0.72494	0.49506	0.49921	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