{"database": "metadata", "table": "run_metadata", "rows": [[34304, "SRR31642050", "SRX27005491", "SRS23470013", "SRP550052", "PRJNA1195551", "scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint", "GSE283763", "Transcriptome Analysis", "Adult mammalian synovial joints have limited regenerative capacity  where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing  we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1  3  7  14  28  and 70 dpjr to capture the major stages of healing post resection.", null, null, null, "Jaw joint cells  14 dpjr  Pooled", "GSM8671776", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells  14 dpjr  Pooled", "CellRanger v6.1.2 10X Genomics  with default parameters was used to generate cell by gene count matrices. Assembly: Danio rerio GRCz11 Supplementary files format and content: matrix  features  barcode files", "Jaw joint", "Whole joint resection surgery was performed on adult zebrafish and collected at 1  3  7  14  28  and 70 days post joint resection. Controls consisted of uninjured samples.", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer\u2019s recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:14 dpjr|batch:2", "GSM8671776", "GSM8671776: Jaw joint cells  14 dpjr  Pooled; Danio rerio; RNA Seq", "GSM8671776 r1", "GSM8671776", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3\u2032 Library & Gel Bead Kit v2 10X Genomics  following the manufacturer's recommendations.  Libraries were sequenced on the NovaSeq 6000 with 101 bp sequencing for Read1  10 bp sequencing for Index1  and 101 bp sequencing for Read2  and 10 bp sequencing for Index2. Each sample was sequenced to a mean read depth of greater than 86 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550052", null, "loader:fastq load.py", "14dpjr_Pooled_L002_I1_001.fastq.gz 14dpjr_Pooled_L002_I2_001.fastq.gz 14dpjr_Pooled_L002_R1_001.fastq.gz 14dpjr_Pooled_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 36987619800.0, 166610900.0, "GSM8671776 r1", "0:10 1:10 2:101 3:101", "A:9731052223;C:6612084734;G:6474066275;T:10837609042;N:589526", 10, 10, 101, 101, 9731052223, 6612084734, 6474066275, 10837609042, 589526, "SRX27005491", "SRS23470013", "SRA2029585", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-08", "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": ["34304"], "units": {}, "query_ms": 10.13949399930425}