{"database": "metadata", "table": "run_metadata", "rows": [[74046, "SRR23360142", "SRX19301395", "SRS16701439", "SRP421311", "PRJNA932229", "Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin", "GSE224695", "Other", "Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish  regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins  suggest hormonal control of epithelial mesenchymal signaling  clarify the signaling network that governs scale papillae development  and identify a critical role for the hypodermis in supporting pigment cell development. Additionally  this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type  eda mutant  bnc2 mutant  and hypothyroid were profiled with with sci RNA seq2.", null, "pubmed:37695017", null, "Multi genotype zebrafish skin snRNAseq", "GSM7029635", null, "tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid|geo loc name:missing|collection date:missing", "Multi genotype zebrafish skin snRNAseq", "The demultiplexing  barcoded processing  gene counting and aggregation were performed using the processing pipeline from Cao et al.  2017 doi: 10.1126/science.aam8940. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated", "Whole skin tissue", "Hypothyroid zebrafish  Tgtg:nVenus v2a nfnBwprt8Tg  underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.", "Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80\u00b0C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.", "Zebrafish were raised at 28.5\u2103 and selected for dissection based on staging landmarks Parichy et al.  2009.", "cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid", "GSM7029635", "GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq", "GSM7029635 r1", "GSM7029635", "1", "Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80\u00b0C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP421311", null, "loader:fastq load.py", "zskin_sciRNA_seq4_R1_merge.fastq.gz zskin_sciRNA_seq4_R2_merge.fastq.gz", "fastq fastq", 33417347600.0, 477390680.0, "GSM7029635 r4", "0:18 1:52", "A:10992313767;C:6719060839;G:6813342549;T:8874815927;N:17814518", 18, 52, null, null, 10992313767, 6719060839, 6813342549, 8874815927, 17814518, "SRX19301395", "SRS16701439", "SRA1657186", "Genome Sciences, University of Washington", "Genome Sciences, University of Washington", 2, 0.0, 0.7972, 0.0, 0.51142, 1.0, 0.84435, null, 0.56962, 18, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2023-02-07", "Larval", "Larval", "Skin", "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": ["74046"], "units": {}, "query_ms": 10.633616999257356}