run_metadata: 52209

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
52209	SRR8992787	SRX5771765	SRS4705624	SRP194294	PRJNA540521	Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores	GSE130526	Other	Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates derived from embryonic neural crest are a useful system for elucidating mechanisms of fate specification pattern formation and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes including zebrafish Danio rerio we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic mutational chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions organelle configurations and genetic requirements. At the organismal level we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together our studies revealed new independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication		pubmed:31138706		Zebrafish fin pigment cells	GSM3741778		tissue:Dorsal and anal fins\|cell type:pigment cells\|treatment:Untreated	Zebrafish fin pigment cells	Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.	Dorsal and anal fins	Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation we extracted distal dorsal fin regions 10 mm standard length SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL 15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence and then cells from transgenic fish were purified according to these gates. All samples were kept on ice except during Liberase incubation and then sorted chilled.	10X genomics V1 protocol following manufacturer recommendations.	Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb a derivative of inbred ABwp Tgtyrp1b:palm mCherrywp.rt11 Tgpnp4a:palmmCherrywp.rt10	cell type:pigment cells\|treatment:Untreated	GSM3741778	GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq	GSM3741778		1	10X genomics V1 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP194294			leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz	fastq fastq	424061944.0	10241510.0	GSM3741778 r1	0:26 1:57	A:119042142;C:89897538;G:98172861;T:116716009;N:233394	26	57			119042142	89897538	98172861	116716009	233394	SRX5771765	SRS4705624	SRA881136	GEO	Parichy Lab, Biology, University of Washington	1	0.33934		0.07693		0.8742		0.51425		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2019-04-30	Multi-stage	Multi-stage	Fin	Surface Structure