run_metadata: 65479

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
65479	SRR15321084	SRX11625562	SRS9659653	SRP330794	PRJNA751418	Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish	GSE181287	Other	We charted the global changes in the epigenetic landscape including DNA methylation and chromatin accessibility during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort in the relatively uncharacterized iridophores we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. Overall design: ATAC seq RNA Seq WGBS were generated for 15 somite NCC 24 hpf NCC 4 dpf 5 dpf Melanophore and 4 dpf 5 dpf Iridophore cells from zebrafish.		pubmed:34607603		RNA seq 24hpf NCC rep1	GSM5494234		tissue:Neural crest cells\|genotype:TgcrestinA:EGFP\|developmental stage:24 hpf\|cell type:Neural crest cells	RNA seq 24hpf NCC rep1	All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter trimmed with cutadapt. RNA seq reads were aligned to danRer10 genome using STAR. WGBS reads were aligned to danRer10 using bismark with standard parameters. omniATAC seq reads were aligned to danRer10 using bwa mem. Genome build: danRer10 Supplementary files format and content: bigWig bedGraph and text files.	Neural crest cells	TgcrestinA:EGFP embryos at designated biological time points were dechorionated with Pronase rinsed with egg water to remove the chorion and collected into 1.5ml Eppendorf tubes on ice. 4 dpf 5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice.	Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.		genotype:TgcrestinA:EGFP\|developmental stage:24 hpf\|cell type:Neural crest cells	GSM5494234	GSM5494234: RNA seq 24hpf NCC rep1; Danio rerio; RNA Seq	GSM5494234		1	Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer's instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.	GEO Accession:GSM5494234	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP330794			RNA_24hpf_GFPpositive_Rep1_R1.fastq.gz RNA_24hpf_GFPpositive_Rep1_R2.fastq.gz	fastq fastq	8541069754.0	57018853.0	GSM5494234 r1	0:74.90 1:74.90	A:1946972443;C:2324912704;G:2313298267;T:1955018508;N:867832	74	74			1946972443	2324912704	2313298267	1955018508	867832	SRX11625562	SRS9659653	SRA1268156	GEO	Ting Wang Lab, Genetics, Washington University in St. Louis	2	0.95998	0.95963	0.02796	0.02758	0.76499	0.76816	0.48357	0.49514	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2021-08-01	Pharyngula	Embryo	Brain	Nervous System