{"database": "metadata", "table": "run_metadata", "rows": [[73981, "SRR23292533", "SRX19235642", "SRS16640049", "SRP420343", "PRJNA930044", "scRNAseq gene expression profile of zebrafish jaw joint cells post IOM ligament transection.", "GSE224197", "Transcriptome Analysis", "Adult zebrafish have the capacity to regenerate craniofacial ligament tissue following a complete transection injury. How this robust skeletal regeneration is achieved remains undefined. Here  we use single cell RNA sequencing to profile RNA expression from FACS sorted cranial neural crest lineage and non cranial neural crest lineage cells including skin and immune populations in the first 3 days post ligament injury. Overall design: To understand the cellular contributors and molecular regulation of craniofacial ligament regeneration in adult zebrafish  we collected jaw joint cells for single cell RNA sequencing following ligament injury. post IOM ligament transection injury and in uninjured and SHAM surgical controls  neural crest lineage cells DsRed and non neural crest lineage cells BFP were isolated using Fluorescence activated cell sorting FACS from jaw joints microdissected from Sox10:Cre;actb2:loxP BFP STOP loxP DsRed transgenic fish and analyzed using scRNAseq.", null, "pubmed:37726321", null, "Sox10Cre BtR IOM 3dplt Red  scRNAseq", "GSM7017325", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 3dplt Red  scRNAseq", "Fastq files were aligned to GRCz11 using CellRanger v3.0.0 from 10X Genomics. Assembly: GRCz11.fa Supplementary files format and content: Processed data for each sample includes CellRanger outputs: barcode  features  and matrix files in tsv format.", "jaw joint", "IOM transection surgery was performed on adult zebrafish and collected at 1 and 3 xxx post injury for 24hplt and 3dplt samples. Controls include uninjured samples and SHAM injury samples. For SHAM  fish were anaesthetized as per experimental samples but only the skin overlying the IOM ligament was lightly nicked. Joints were collected 1 and 3 days post surgery for 24hSHAM and 3dSHAM samples.", "Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.", null, "tissue:jaw joint|age:3 5mpf adult|cell type:CNCC enriched|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017325", "GSM7017325: Sox10Cre BtR IOM 3dplt Red  scRNAseq; Danio rerio; RNA Seq", "GSM7017325 r1", "GSM7017325", "1", "Microdissected joints were mechanically and enzymatically dissociated prior to FACS sorting with either enrichment for DsRed+ cranial neural crest CNCC lineage cells or no enrichment in BFP+ libraries. FACS sorted cells were processed using the 10X Chromium controller for single cell profiling. Barcoded single cell cDNA library constuction performed as per manufacturer's instructions using the 10X scRNAseq Kit v2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP420343", null, null, "Sox10Cre_BtR_IOM_3dplt_DsRed-2_S34_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-2_S34_L001_R2_001.fastq.gz", "fastq fastq", 3137844278.0, 21279993.0, "GSM7017325 r2", "0:27 1:120.46", "A:870482223;C:695563498;G:723319796;T:845918600;N:2560161", 27, 120, null, null, 870482223, 695563498, 723319796, 845918600, 2560161, "SRX19235642", "SRS16640049", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00159, 0.92488, 0.00061, 0.12748, 0.99695, 0.85307, 0.45077, 0.49755, 27, 118, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-31", "Adult", "Adult", "Jaw", "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": ["73981"], "units": {}, "query_ms": 7.432142000197928}