{"database": "metadata", "table": "run_metadata", "rows": [[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\u2014leucophores\u2014one 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", null, "pubmed:31138706", null, "Zebrafish fin pigment cells", "GSM3741778", null, "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\u00b0C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 \u03bcm 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 \u03bcg/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", null, "1", "10X genomics V1 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP194294", null, null, "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, null, null, 119042142, 89897538, 98172861, 116716009, 233394, "SRX5771765", "SRS4705624", "SRA881136", "GEO", "Parichy Lab, Biology, University of Washington", 1, 0.33934, null, 0.07693, null, 0.8742, null, 0.51425, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-04-30", "Multi-stage", "Multi-stage", "Fin", "Surface Structure"]], "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": ["52209"], "units": {}, "query_ms": 10.283430005074479}