run_metadata: 60611

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
60611	SRR12435890	SRX8931585	SRS7187993	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536		RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2	GSM4724532		tissue:whole embryo\|developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	GSM4724532	GSM4724532: RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2; Danio rerio; RNA Seq	GSM4724532		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724532	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500		SRP277167			RNAseq_48h_ctcf_p53MO_rep2_1.fq.gz	fastq	2622498950.0	52449979.0	GSM4724532 r1	0:50	A:683425987;C:612438973;G:639683260;T:686950730;N:0	50				683425987	612438973	639683260	686950730	0	SRX8931585	SRS7187993	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94822		0.10163		0.69954		0.4758		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures