{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:34607603", null, "RNA seq 24hpf NCC  rep1", "GSM5494234", null, "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\u2019s 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.", null, "genotype:TgcrestinA:EGFP|developmental stage:24 hpf|cell type:Neural crest cells", "GSM5494234", "GSM5494234: RNA seq 24hpf NCC  rep1; Danio rerio; RNA Seq", "GSM5494234", null, "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", null, "SRP330794", null, null, "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, null, null, 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", null, "United States", "2021-08-01", "Pharyngula", "Embryo", "Brain", "Nervous System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["65479"], "units": {}, "query_ms": 8.28948200069135}