run_metadata: 44531

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
44531	SRR7868771	SRX4707944	SRS3793647	SRP124607	PRJNA417594	From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo	GSE106676	Other	The neural crest NC is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here we perform NC specific transcriptional and epigenomic profiling of foxd3 mutant versus wild type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin ChIP and single cell profiles of foxd3 expressing premigratory NC our analysis shows that during early steps of NC formation foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re arranging the chromatin landscape opening cis regulatory elements and reshuffling nucleosomes. Strikingly foxd3 then gradually switches from an activator to its previously well described role as a transcriptional repressor. Taken together these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from 'permissive' to 'repressive' nucleosome/chromatin organisation to maintain multipotency and define cell fates. Overall design: Examination of RNA seq ATAC seq histone ChIP seq Biotin ChIP seq in wild type and foxd3 mutant context at epib stages and in neural crest cells; single cell RNA seq		pubmed:30513303;pubmed:33111104		Cit 8ss RNAseq	GSM3393489		source name:Cit 8ss RNAseq\|strain:Gtfoxd3 Citrinect110a\|tissue:Embryo\|development stage:8 somites\|cell type:Neural crest foxd3 cells\|isolation method:Dissociations and FACS\|treatment: \|amplification:Illumina Nextera XT library preparation kit\|assay:RNA seq	Cit 8ss RNAseq	ChIP seq and ATAC seq reads were mapped using bowtie v.1.0.0 ChIP seq and ATAC seq: duplicates were removed using MarkDuplicates picard tools/1.83 Input reads were normalised to the same number of ChIP reads by random down sampling using samtools/1.1 ChIP peak calling was performed using Homer v.4.7 findPeaks script using size 200 minDist 1500 parameters. ATAC seq: All samples were randomly down sampled to the lowest read containing sample 10 443 726 using samtools/1.1. ATAC seq: control tripilactes were merged and experimental triplicate BAM files were merged and sorted using samtools/1.1 ATAC seq:k means clustering of ATAC seq signal was carried out using SeqMINER software as described Ye et al. 2011 using 3.1 enhancer cluster ATAC seq peaks and all pulled foxd3 Biotin ChIP peaks as references for clustering. RNA seq reads were mapped using STAR v.2.4.2a Genome build: danRer10	Cit 8ss RNAseq		Illumina Nextera XT library preparation kit		strain:Gtfoxd3 Citrinect110a\|tissue:Embryo\|development stage:8 somites\|cell type:Neural crest foxd3 cells\|isolation method:Dissociations and FACS\|treatment: \|amplification: Illumina Nextera XT library preparation kit\|assay:RNA seq	GSM3393489	GSM3393489: Cit 8ss RNAseq; Danio rerio; RNA Seq	GSM3393489		1	Illumina Nextera XT library preparation kit	GEO Accession:GSM3393489	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP124607			WTCHG_116006_201_1.fastq.gz WTCHG_116006_201_2.fastq.gz	fastq fastq	4981486000.0	24907430.0	GSM3393489 r1	0:100 1:100	A:1360272094;C:1090492330;G:1142929599;T:1387078225;N:713752	100	100			1360272094	1090492330	1142929599	1387078225	713752	SRX4707944	SRS3793647	SRA629218	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.94827	0.92512	0.12816	0.13505	0.74554	0.77613	0.51991	0.49505	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only		United Kingdom	2018-09-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures