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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 28 dpjr Pooled", "GSM8671778", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:28 dpjr|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells 28 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:28 dpjr|batch:2", "GSM8671778", "GSM8671778: Jaw joint cells 28 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671778 r1", "GSM8671778", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Single Animal", "GSM8671777", 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 Single Animal", "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", "GSM8671777", "GSM8671777: Jaw joint cells 14 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671777 r1", "GSM8671777", "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_Single_Animal_L002_I1_001.fastq.gz 14dpjr_Single_Animal_L002_I2_001.fastq.gz 14dpjr_Single_Animal_L002_R1_001.fastq.gz 14dpjr_Single_Animal_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 37035287196.0, 166825618.0, "GSM8671777 r1", "0:10 1:10 2:101 3:101", "A:9648639338;C:6931863960;G:6677103016;T:10440574408;N:594114", 10, 10, 101, 101, 9648639338, 6931863960, 6677103016, 10440574408, 594114, "SRX27005492", "SRS23470014", "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"], [34303, "SRR31642049", "SRX27005492", "SRS23470014", "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 Single Animal", "GSM8671777", 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 Single Animal", "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", "GSM8671777", "GSM8671777: Jaw joint cells 14 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671777 r1", "GSM8671777", "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. 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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"], [34305, "SRR31642051", "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_L003_I1_001.fastq.gz 14dpjr_Pooled_L003_I2_001.fastq.gz 14dpjr_Pooled_L003_R1_001.fastq.gz 14dpjr_Pooled_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 37823124792.0, 170374436.0, "GSM8671776 r2", "0:10 1:10 2:101 3:101", "A:10018290148;C:6801679608;G:6619700517;T:10975336592;N:629207", 10, 10, 101, 101, 10018290148, 6801679608, 6619700517, 10975336592, 629207, "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"], [34306, "SRR31642052", "SRX27005490", "SRS23470012", "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 7 dpjr Single Animal", "GSM8671775", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 7 dpjr Single Animal", "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:7 dpjr|batch:1", "GSM8671775", "GSM8671775: Jaw joint cells 7 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671775 r1", "GSM8671775", "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. 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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 7 dpjr Single Animal", "GSM8671775", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 7 dpjr Single Animal", "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:7 dpjr|batch:1", "GSM8671775", "GSM8671775: Jaw joint cells 7 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671775 r1", "GSM8671775", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 7 dpjr Pooled", "GSM8671774", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 7 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:7 dpjr|batch:1", "GSM8671774", "GSM8671774: Jaw joint cells 7 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671774 r1", "GSM8671774", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 7 dpjr Pooled", "GSM8671774", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:7 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 7 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:7 dpjr|batch:1", "GSM8671774", "GSM8671774: Jaw joint cells 7 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671774 r1", "GSM8671774", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 3 dpjr Single Animal", "GSM8671773", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 3 dpjr Single Animal", "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:3 dpjr|batch:1", "GSM8671773", "GSM8671773: Jaw joint cells 3 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671773 r1", "GSM8671773", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 3 dpjr Single Animal", "GSM8671773", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 3 dpjr Single Animal", "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:3 dpjr|batch:1", "GSM8671773", "GSM8671773: Jaw joint cells 3 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671773 r1", "GSM8671773", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 3 dpjr Pooled", "GSM8671772", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 3 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:3 dpjr|batch:1", "GSM8671772", "GSM8671772: Jaw joint cells 3 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671772 r1", "GSM8671772", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 3 dpjr Pooled", "GSM8671772", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:3 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 3 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:3 dpjr|batch:1", "GSM8671772", "GSM8671772: Jaw joint cells 3 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671772 r1", "GSM8671772", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 1 dpjr Single Animal", "GSM8671771", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 1 dpjr Single Animal", "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:1 dpjr|batch:1", "GSM8671771", "GSM8671771: Jaw joint cells 1 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671771 r1", "GSM8671771", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 1 dpjr Single Animal", "GSM8671771", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 1 dpjr Single Animal", "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:1 dpjr|batch:1", "GSM8671771", "GSM8671771: Jaw joint cells 1 dpjr Single Animal; Danio rerio; RNA Seq", "GSM8671771 r1", "GSM8671771", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 1 dpjr Pooled", "GSM8671770", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 1 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:1 dpjr|batch:1", "GSM8671770", "GSM8671770: Jaw joint cells 1 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671770 r1", "GSM8671770", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 1 dpjr Pooled", "GSM8671770", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:1 dpjr|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells 1 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:1 dpjr|batch:1", "GSM8671770", "GSM8671770: Jaw joint cells 1 dpjr Pooled; Danio rerio; RNA Seq", "GSM8671770 r1", "GSM8671770", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Uninjured Single Animal 2", "GSM8671769", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells Uninjured Single Animal 2", "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:Uninjured|batch:2", "GSM8671769", "GSM8671769: Jaw joint cells Uninjured Single Animal 2; Danio rerio; RNA Seq", "GSM8671769 r1", "GSM8671769", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Uninjured Single Animal 2", "GSM8671769", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells Uninjured Single Animal 2", "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:Uninjured|batch:2", "GSM8671769", "GSM8671769: Jaw joint cells Uninjured Single Animal 2; Danio rerio; RNA Seq", "GSM8671769 r1", "GSM8671769", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Uninjured Single Animal 1", "GSM8671768", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells Uninjured Single Animal 1", "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:Uninjured|batch:1", "GSM8671768", "GSM8671768: Jaw joint cells Uninjured Single Animal 1; Danio rerio; RNA Seq", "GSM8671768 r1", "GSM8671768", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Uninjured Single Animal 1", "GSM8671768", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:1|geo loc name:missing|collection date:missing", "Jaw joint cells Uninjured Single Animal 1", "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:Uninjured|batch:1", "GSM8671768", "GSM8671768: Jaw joint cells Uninjured Single Animal 1; Danio rerio; RNA Seq", "GSM8671768 r1", "GSM8671768", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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. 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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:Uninjured|batch:2", "GSM8671767", "GSM8671767: Jaw joint cells Uninjured Pooled; Danio rerio; RNA Seq", "GSM8671767 r1", "GSM8671767", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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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 Uninjured Pooled", "GSM8671767", null, "source name:Jaw joint|tissue:Jaw joint|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP|age:3 mpf 6 mpf|treatment:Uninjured|batch:2|geo loc name:missing|collection date:missing", "Jaw joint cells Uninjured 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:Uninjured|batch:2", "GSM8671767", "GSM8671767: Jaw joint cells Uninjured Pooled; Danio rerio; RNA Seq", "GSM8671767 r1", "GSM8671767", "1", "Jaw joint tissue was microdissected and subjected to mechanical and enzymatic dissociation. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "trps1:eGFP enriched", "GSM5587035", null, "source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "trps1:eGFP enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "trps1:eGFP enriched", "GSM5587035", null, "source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "trps1:eGFP enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587035", "GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq", "GSM5587035", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "trps1:eGFP enriched", "GSM5587035", null, "source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "trps1:eGFP enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587035", "GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq", "GSM5587035", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "trps1:eGFP enriched", "GSM5587035", null, "source name:Adult Jaw Joint|cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "trps1:eGFP enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:trps1:eGFP positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587035", "GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq", "GSM5587035", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "sox10:DsRed enriched", "GSM5587034", null, "source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "sox10:DsRed enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587034", "GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq", "GSM5587034", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. 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Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "sox10:DsRed enriched", "GSM5587034", null, "source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "sox10:DsRed enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587034", "GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq", "GSM5587034", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", "GEO Accession:GSM5587034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337784", null, null, "sox10enriched-2_R1_001.fastq.gz sox10enriched-2_R2_001.fastq.gz", "fastq fastq", 2268301929.0, 15392389.0, "GSM5587034 r2", "0:27 1:120.37", "A:645886696;C:468225565;G:493153165;T:659172922;N:1863581", 27, 120, null, null, 645886696, 468225565, 493153165, 659172922, 1863581, "SRX12254436", "SRS10230008", "SRA1296796", "GEO", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.0032, 0.90785, 0.00116, 0.19777, 0.99423, 0.84847, 0.44783, 0.49424, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-09-19", "Adult", "Adult", "Jaw", "Surface Structure"], [66184, "SRR15964628", "SRX12254436", "SRS10230008", "SRP337784", "PRJNA764519", "Single Cell Analysis of adult zebrafish jaw joint", "GSE184403", "Transcriptome Analysis", "To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "sox10:DsRed enriched", "GSM5587034", null, "source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "sox10:DsRed enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587034", "GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq", "GSM5587034", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", "GEO Accession:GSM5587034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337784", null, null, "sox10enriched-3_R1_001.fastq.gz sox10enriched-3_R2_001.fastq.gz", "fastq fastq", 2826349266.0, 19178616.0, "GSM5587034 r3", "0:27 1:120.37", "A:803669086;C:587771264;G:615160821;T:817438779;N:2309316", 27, 120, null, null, 803669086, 587771264, 615160821, 817438779, 2309316, "SRX12254436", "SRS10230008", "SRA1296796", "GEO", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00361, 0.90664, 0.00122, 0.19569, 0.99328, 0.85173, 0.44136, 0.49393, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-09-19", "Adult", "Adult", "Jaw", "Surface Structure"], [66185, "SRR15964629", "SRX12254436", "SRS10230008", "SRP337784", "PRJNA764519", "Single Cell Analysis of adult zebrafish jaw joint", "GSE184403", "Transcriptome Analysis", "To profile the diversity of cell types present in adult zebrafish synovial joints we performed single cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal connective tissue and fibroblast subtypes including a joint specific periosteal population. Overall design: Single cell RNA sequencing of FACS isolated zebrafish joint cells trps1:eGFP enriched; sox10:DsRed enriched from 3 mpf microdissected jaw joints", null, "pubmed:35127702", null, "sox10:DsRed enriched", "GSM5587034", null, "source name:Adult Jaw Joint|cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "sox10:DsRed enriched", "Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes Genome build: z11 Supplementary files format and content: barcodes features and matrix files from Cell Ranger alignment", "Adult Jaw Joint", null, "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", null, "cell type:sox10:DsRed positive joint cell|age:3 mpf|tissue:Jaw joint", "GSM5587034", "GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq", "GSM5587034", null, "1", "50 micro dissected jaw joints from 3 mpf sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed positive +/ GFP and GFP positive populations. Single cells were processed through the 10X chromium controller. Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell three prime Library and Gel Bead Kit v.2. standard protocol", "GEO Accession:GSM5587034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337784", null, null, "sox10enriched-4_R1_001.fastq.gz sox10enriched-4_R2_001.fastq.gz", "fastq fastq", 2932941460.0, 19904579.0, "GSM5587034 r4", "0:27 1:120.35", "A:832669575;C:611997497;G:644091515;T:841813951;N:2368922", 27, 120, null, null, 832669575, 611997497, 644091515, 841813951, 2368922, "SRX12254436", "SRS10230008", "SRA1296796", "GEO", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00343, 0.91021, 0.00112, 0.19104, 0.99375, 0.84883, 0.49557, 0.50272, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-09-19", "Adult", "Adult", "Jaw", "Surface Structure"], [70844, "SRR20737630", "SRX16758028", "SRS14385048", "SRP389175", "PRJNA864829", "Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos", "GSE210251", "Other", "The functional jaw is composed of multiple connective tissues including skeletal components bone cartilage and teeth tendon ligament and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.", null, "pubmed:36905926", null, "Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq", "GSM6424705", null, "source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI / GFP+", "Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq", "Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer\u2019s instructions 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries both Read1 and Read2 were extended to 60 cycles whereas for sequencing snRNAseq libraries Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer\u2019s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.", "Jaw mesenchyme", null, "Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer\u2019s solution 116mM NaCl 2.6mM KCl 5mM HEPES pH 7.0 followed by dissociation at 28.5\u2009\u00b0C for 40\u2009min by mechanical nutating and pipetting every 5\u2009min and enzymatic in pre warmed protease solution 0.25% trypsin 1\u2009mM EDTA pH 8.0 and 20 mg/mL Collagenase D from stock of 400\u2009mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min 2000 rpm at 4\u00b0C and washed by suspension solution 1% FBS 0.8mM CaCl2 50U/ml Penicillin 0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4\u00b0C. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomics protocol CG000169 low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min 300 rcf at 4oC and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a\u00a0fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer\u2019s instructions accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.", "All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5\u00b0C with health and water conditions monitored daily.", "tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI / GFP+", "GSM6424705", "GSM6424705: Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq", "GSM6424705 r1", "GSM6424705", "1", "Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl 2.6mM KCl 5mM HEPES pH 7.0 followed by dissociation at 28.5\u2009\u00b0C for 40\u2009min by mechanical nutating and pipetting every 5\u2009min and enzymatic in pre warmed protease solution 0.25% trypsin 1\u2009mM EDTA pH 8.0 and 20 mg/mL Collagenase D from stock of 400\u2009mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min 2000 rpm at 4\u00b0C and washed by suspension solution 1% FBS 0.8mM CaCl2 50U/ml Penicillin 0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4\u00b0C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics protocol CG000169 low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min 300 rcf at 4oC and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP389175", null, "loader:fastq load.py", "Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R1_001.fastq.gz Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R2_001.fastq.gz", "fastq fastq", 24616183454.0, 187429180.0, "GSM6424705 r1", "0:29 1:102.34", "A:5661562219;C:4278027880;G:4357175731;T:5550818399;N:4768599225", 29, 102, null, null, 5661562219, 4278027880, 4357175731, 5550818399, 4768599225, "SRX16758028", "SRS14385048", "SRA1467000", "Stem Cell Department at USC", "Stem Cell Department at USC", 2, 0.01084, 0.91331, 0.00616, 0.27551, 0.99153, 0.84447, 0.51001, 0.63176, 29, 102, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-08-01", "Hatching", "Embryo", "Jaw", "Surface Structure"], [70845, "SRR20737632", "SRX16758026", "SRS14385046", "SRP389175", "PRJNA864829", "Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos", "GSE210251", "Other", "The functional jaw is composed of multiple connective tissues including skeletal components bone cartilage and teeth tendon ligament and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.", null, "pubmed:36905926", null, "Multiome control nr5a2 GFP 2.5dpf head snRNA seq", "GSM6424703", null, "source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie / GFP+", "Multiome control nr5a2 GFP 2.5dpf head snRNA seq", "Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer\u2019s instructions 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries both Read1 and Read2 were extended to 60 cycles whereas for sequencing snRNAseq libraries Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer\u2019s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.", "Jaw mesenchyme", null, "Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer\u2019s solution 116mM NaCl 2.6mM KCl 5mM HEPES pH 7.0 followed by dissociation at 28.5\u2009\u00b0C for 40\u2009min by mechanical nutating and pipetting every 5\u2009min and enzymatic in pre warmed protease solution 0.25% trypsin 1\u2009mM EDTA pH 8.0 and 20 mg/mL Collagenase D from stock of 400\u2009mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min 2000 rpm at 4\u00b0C and washed by suspension solution 1% FBS 0.8mM CaCl2 50U/ml Penicillin 0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4\u00b0C. Nuclei isolation was performed per manufacturer\u2019s instructions 10X Genomics protocol CG000169 low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min 300 rcf at 4oC and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a\u00a0fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer\u2019s instructions accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.", "All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5\u00b0C with health and water conditions monitored daily.", "tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie / GFP+", "GSM6424703", "GSM6424703: Multiome control nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq", "GSM6424703 r1", "GSM6424703", "1", "Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl 2.6mM KCl 5mM HEPES pH 7.0 followed by dissociation at 28.5\u2009\u00b0C for 40\u2009min by mechanical nutating and pipetting every 5\u2009min and enzymatic in pre warmed protease solution 0.25% trypsin 1\u2009mM EDTA pH 8.0 and 20 mg/mL Collagenase D from stock of 400\u2009mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min 2000 rpm at 4\u00b0C and washed by suspension solution 1% FBS 0.8mM CaCl2 50U/ml Penicillin 0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4\u00b0C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics protocol CG000169 low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min 300 rcf at 4oC and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP389175", null, "loader:fastq load.py", "Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R1_001.fastq.gz Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R2_001.fastq.gz", "fastq fastq", 64154124610.0, 487905462.0, "GSM6424703 r1", "0:29 1:102.49", "A:18612889696;C:13758862487;G:13948126717;T:17774530698;N:59715012", 29, 102, null, null, 18612889696, 13758862487, 13948126717, 17774530698, 59715012, "SRX16758026", "SRS14385046", "SRA1467000", "Stem Cell Department at USC", "Stem Cell Department at USC", 2, 0.01181, 0.86488, 0.00641, 0.29997, 0.99093, 0.80795, 0.50941, 0.6767, 29, 102, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-08-01", "Hatching", "Embryo", "Jaw", "Surface Structure"], [73980, "SRR23292532", "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-1_S33_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-1_S33_L001_R2_001.fastq.gz", "fastq fastq", 3212586883.0, 21782952.0, "GSM7017325 r1", "0:27 1:120.48", "A:889247747;C:712836063;G:736196241;T:871677201;N:2629631", 27, 120, null, null, 889247747, 712836063, 736196241, 871677201, 2629631, "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, 0.00151, 0.92087, 0.0007, 0.13437, 0.99748, 0.87065, 0.41025, 0.52913, 27, 121, "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"], [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"], [73982, "SRR23292534", "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-3_S35_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-3_S35_L001_R2_001.fastq.gz", "fastq fastq", 4071005433.0, 27610532.0, "GSM7017325 r3", "0:27 1:120.44", "A:1139555452;C:904968992;G:940567540;T:1082637805;N:3275644", 27, 120, null, null, 1139555452, 904968992, 940567540, 1082637805, 3275644, "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, 0.0015, 0.92439, 0.00071, 0.12885, 0.9976, 0.8617, 0.46451, 0.53839, 27, 121, "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"], [73983, "SRR23292535", "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-4_S36_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_DsRed-4_S36_L001_R2_001.fastq.gz", "fastq fastq", 3556411984.0, 24118414.0, "GSM7017325 r4", "0:27 1:120.46", "A:985423514;C:790585258;G:820334327;T:957180576;N:2888309", 27, 120, null, null, 985423514, 790585258, 820334327, 957180576, 2888309, "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, 0.92458, 0.00072, 0.12712, 0.99744, 0.85429, 0.39759, 0.50442, 27, 119, "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"], [73984, "SRR23292536", "SRX19235641", "SRS16640048", "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 Blue scRNAseq", "GSM7017324", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 3dplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017324", "GSM7017324: Sox10Cre BtR IOM 3dplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017324 r1", "GSM7017324", "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_BFP-1_S29_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_BFP-1_S29_L001_R2_001.fastq.gz", "fastq fastq", 5128578244.0, 34770233.0, "GSM7017324 r1", "0:27 1:120.50", "A:1445900889;C:1122404751;G:1138509112;T:1417562371;N:4201121", 27, 120, null, null, 1445900889, 1122404751, 1138509112, 1417562371, 4201121, "SRX19235641", "SRS16640048", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.0019, 0.90605, 0.00095, 0.16283, 0.99722, 0.86344, 0.46739, 0.57415, 27, 120, "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"], [73985, "SRR23292537", "SRX19235641", "SRS16640048", "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 Blue scRNAseq", "GSM7017324", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 3dplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017324", "GSM7017324: Sox10Cre BtR IOM 3dplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017324 r1", "GSM7017324", "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_BFP-2_S30_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_BFP-2_S30_L001_R2_001.fastq.gz", "fastq fastq", 5065106361.0, 34347749.0, "GSM7017324 r2", "0:27 1:120.47", "A:1425022693;C:1108740806;G:1140300932;T:1386898454;N:4143476", 27, 120, null, null, 1425022693, 1108740806, 1140300932, 1386898454, 4143476, "SRX19235641", "SRS16640048", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00178, 0.91213, 0.0009, 0.15057, 0.99728, 0.84114, 0.51461, 0.5822, 27, 121, "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"], [73986, "SRR23292538", "SRX19235641", "SRS16640048", "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 Blue scRNAseq", "GSM7017324", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 3dplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017324", "GSM7017324: Sox10Cre BtR IOM 3dplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017324 r1", "GSM7017324", "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_BFP-3_S31_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_BFP-3_S31_L001_R2_001.fastq.gz", "fastq fastq", 6533108951.0, 44301913.0, "GSM7017324 r3", "0:27 1:120.47", "A:1841801865;C:1426610652;G:1466708577;T:1792638816;N:5349041", 27, 120, null, null, 1841801865, 1426610652, 1466708577, 1792638816, 5349041, "SRX19235641", "SRS16640048", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00198, 0.91199, 0.00091, 0.15309, 0.99675, 0.84264, 0.48803, 0.57947, 27, 121, "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"], [73987, "SRR23292539", "SRX19235641", "SRS16640048", "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 Blue scRNAseq", "GSM7017324", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 3dplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017324", "GSM7017324: Sox10Cre BtR IOM 3dplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017324 r1", "GSM7017324", "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_BFP-4_S32_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dplt_BFP-4_S32_L001_R2_001.fastq.gz", "fastq fastq", 7429853519.0, 50387625.0, "GSM7017324 r4", "0:27 1:120.45", "A:2093566694;C:1627531666;G:1681380167;T:2021361003;N:6013989", 27, 120, null, null, 2093566694, 1627531666, 1681380167, 2021361003, 6013989, "SRX19235641", "SRS16640048", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00182, 0.91485, 0.00082, 0.14827, 0.99695, 0.83997, 0.50515, 0.57637, 27, 120, "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"], [73988, "SRR23292540", "SRX19235640", "SRS16640047", "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 24hplt Red scRNAseq", "GSM7017323", 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 24hplt 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", "GSM7017323", "GSM7017323: Sox10Cre BtR IOM 24hplt Red scRNAseq; Danio rerio; RNA Seq", "GSM7017323 r1", "GSM7017323", "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_24hplt_Red-1_S13_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Red-1_S13_L001_R2_001.fastq.gz", "fastq fastq", 540330480.0, 3665407.0, "GSM7017323 r1", "0:27 1:120.41", "A:155935239;C:112933414;G:125480506;T:145069042;N:912279", 27, 120, null, null, 155935239, 112933414, 125480506, 145069042, 912279, "SRX19235640", "SRS16640047", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00194, 0.93353, 0.00076, 0.11452, 0.99659, 0.84226, 0.49771, 0.52855, 27, 120, "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"], [73989, "SRR23292541", "SRX19235640", "SRS16640047", "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 24hplt Red scRNAseq", "GSM7017323", 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 24hplt 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", "GSM7017323", "GSM7017323: Sox10Cre BtR IOM 24hplt Red scRNAseq; Danio rerio; RNA Seq", "GSM7017323 r1", "GSM7017323", "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_24hplt_Red-2_S14_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Red-2_S14_L001_R2_001.fastq.gz", "fastq fastq", 588121818.0, 3989625.0, "GSM7017323 r2", "0:27 1:120.41", "A:169709811;C:122804703;G:136642899;T:157981691;N:982714", 27, 120, null, null, 169709811, 122804703, 136642899, 157981691, 982714, "SRX19235640", "SRS16640047", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00223, 0.93308, 0.00078, 0.11391, 0.99624, 0.84348, 0.4382, 0.5488, 27, 120, "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"], [73990, "SRR23292542", "SRX19235640", "SRS16640047", "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 24hplt Red scRNAseq", "GSM7017323", 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 24hplt 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", "GSM7017323", "GSM7017323: Sox10Cre BtR IOM 24hplt Red scRNAseq; Danio rerio; RNA Seq", "GSM7017323 r1", "GSM7017323", "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_24hplt_Red-3_S15_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Red-3_S15_L001_R2_001.fastq.gz", "fastq fastq", 512261066.0, 3474928.0, "GSM7017323 r3", "0:27 1:120.42", "A:147415177;C:107153129;G:119475615;T:137350960;N:866185", 27, 120, null, null, 147415177, 107153129, 119475615, 137350960, 866185, "SRX19235640", "SRS16640047", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00231, 0.93469, 0.00077, 0.11629, 0.99584, 0.84699, 0.52613, 0.54536, 27, 120, "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"], [73991, "SRR23292543", "SRX19235640", "SRS16640047", "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 24hplt Red scRNAseq", "GSM7017323", 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 24hplt 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", "GSM7017323", "GSM7017323: Sox10Cre BtR IOM 24hplt Red scRNAseq; Danio rerio; RNA Seq", "GSM7017323 r1", "GSM7017323", "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_24hplt_Red-4_S16_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Red-4_S16_L001_R2_001.fastq.gz", "fastq fastq", 391834759.0, 2658174.0, "GSM7017323 r4", "0:27 1:120.41", "A:113118161;C:81782934;G:91282994;T:104997791;N:652879", 27, 120, null, null, 113118161, 81782934, 91282994, 104997791, 652879, "SRX19235640", "SRS16640047", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00213, 0.93317, 0.00074, 0.11599, 0.99636, 0.84437, 0.53906, 0.5393, 27, 121, "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"], [73992, "SRR23292544", "SRX19235639", "SRS16640046", "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 24hplt Blue scRNAseq", "GSM7017322", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 24hplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017322", "GSM7017322: Sox10Cre BtR IOM 24hplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017322 r1", "GSM7017322", "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_24hplt_Blue-1_S9_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Blue-1_S9_L001_R2_001.fastq.gz", "fastq fastq", 7263817079.0, 49258946.0, "GSM7017322 r1", "0:27 1:120.46", "A:2100144550;C:1491191777;G:1653894733;T:2006228244;N:12357775", 27, 120, null, null, 2100144550, 1491191777, 1653894733, 2006228244, 12357775, "SRX19235639", "SRS16640046", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00368, 0.91091, 0.00135, 0.15684, 0.99466, 0.82731, 0.5, 0.57586, 27, 120, "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"], [73993, "SRR23292545", "SRX19235639", "SRS16640046", "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 24hplt Blue scRNAseq", "GSM7017322", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 24hplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017322", "GSM7017322: Sox10Cre BtR IOM 24hplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017322 r1", "GSM7017322", "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_24hplt_Blue-2_S10_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Blue-2_S10_L001_R2_001.fastq.gz", "fastq fastq", 5225711832.0, 35437304.0, "GSM7017322 r2", "0:27 1:120.46", "A:1513630438;C:1070631991;G:1185409561;T:1447157372;N:8882470", 27, 120, null, null, 1513630438, 1070631991, 1185409561, 1447157372, 8882470, "SRX19235639", "SRS16640046", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00332, 0.91111, 0.00118, 0.15593, 0.99476, 0.8269, 0.4811, 0.57679, 27, 120, "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"], [73994, "SRR23292546", "SRX19235639", "SRS16640046", "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 24hplt Blue scRNAseq", "GSM7017322", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 24hplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017322", "GSM7017322: Sox10Cre BtR IOM 24hplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017322 r1", "GSM7017322", "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_24hplt_Blue-3_S11_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Blue-3_S11_L001_R2_001.fastq.gz", "fastq fastq", 7231978745.0, 49042771.0, "GSM7017322 r3", "0:27 1:120.46", "A:2088991701;C:1488148171;G:1648761180;T:1993794690;N:12283003", 27, 120, null, null, 2088991701, 1488148171, 1648761180, 1993794690, 12283003, "SRX19235639", "SRS16640046", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00357, 0.90999, 0.00136, 0.15185, 0.99466, 0.82773, 0.48292, 0.57234, 27, 120, "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"], [73995, "SRR23292547", "SRX19235639", "SRS16640046", "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 24hplt Blue scRNAseq", "GSM7017322", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "Sox10Cre BtR IOM 24hplt Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:ligament transection", "GSM7017322", "GSM7017322: Sox10Cre BtR IOM 24hplt Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017322 r1", "GSM7017322", "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_24hplt_Blue-4_S12_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hplt_Blue-4_S12_L001_R2_001.fastq.gz", "fastq fastq", 6362603214.0, 43146692.0, "GSM7017322 r4", "0:27 1:120.46", "A:1835608926;C:1307215426;G:1452909985;T:1756018170;N:10850707", 27, 120, null, null, 1835608926, 1307215426, 1452909985, 1756018170, 10850707, "SRX19235639", "SRS16640046", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00366, 0.91006, 0.00116, 0.1551, 0.99409, 0.82828, 0.52483, 0.5624, 27, 121, "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"], [73996, "SRR23292548", "SRX19235638", "SRS16640045", "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 3dSHAM Red scRNAseq", "GSM7017321", 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:SHAM injury", "Sox10Cre BtR IOM 3dSHAM 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:SHAM injury", "GSM7017321", "GSM7017321: Sox10Cre BtR IOM 3dSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017321 r1", "GSM7017321", "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_3dSHAM_DsRed-1_S25_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_DsRed-1_S25_L001_R2_001.fastq.gz", "fastq fastq", 6120714740.0, 41511106.0, "GSM7017321 r1", "0:27 1:120.45", "A:1714370972;C:1327758315;G:1387690148;T:1685887076;N:5008229", 27, 120, null, null, 1714370972, 1327758315, 1387690148, 1685887076, 5008229, "SRX19235638", "SRS16640045", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00174, 0.91667, 0.00068, 0.1616, 0.99691, 0.85005, 0.43902, 0.51229, 27, 120, "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"], [73997, "SRR23292549", "SRX19235638", "SRS16640045", "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 3dSHAM Red scRNAseq", "GSM7017321", 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:SHAM injury", "Sox10Cre BtR IOM 3dSHAM 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:SHAM injury", "GSM7017321", "GSM7017321: Sox10Cre BtR IOM 3dSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017321 r1", "GSM7017321", "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_3dSHAM_DsRed-2_S26_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_DsRed-2_S26_L001_R2_001.fastq.gz", "fastq fastq", 4001907942.0, 27139901.0, "GSM7017321 r2", "0:27 1:120.45", "A:1119069117;C:871705095;G:909847660;T:1098029699;N:3256371", 27, 120, null, null, 1119069117, 871705095, 909847660, 1098029699, 3256371, "SRX19235638", "SRS16640045", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00179, 0.91776, 0.00079, 0.1617, 0.99705, 0.85561, 0.44791, 0.5115, 27, 120, "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"], [73998, "SRR23292550", "SRX19235638", "SRS16640045", "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 3dSHAM Red scRNAseq", "GSM7017321", 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:SHAM injury", "Sox10Cre BtR IOM 3dSHAM 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:SHAM injury", "GSM7017321", "GSM7017321: Sox10Cre BtR IOM 3dSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017321 r1", "GSM7017321", "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_3dSHAM_DsRed-3_S27_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_DsRed-3_S27_L001_R2_001.fastq.gz", "fastq fastq", 3629342210.0, 24610225.0, "GSM7017321 r3", "0:27 1:120.47", "A:1015815534;C:788259471;G:818604913;T:1003691058;N:2971234", 27, 120, null, null, 1015815534, 788259471, 818604913, 1003691058, 2971234, "SRX19235638", "SRS16640045", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00179, 0.91476, 0.0007, 0.16723, 0.99667, 0.86537, 0.42452, 0.51614, 27, 121, "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"], [73999, "SRR23292551", "SRX19235638", "SRS16640045", "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 3dSHAM Red scRNAseq", "GSM7017321", 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:SHAM injury", "Sox10Cre BtR IOM 3dSHAM 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:SHAM injury", "GSM7017321", "GSM7017321: Sox10Cre BtR IOM 3dSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017321 r1", "GSM7017321", "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_3dSHAM_DsRed-4_S28_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_DsRed-4_S28_L001_R2_001.fastq.gz", "fastq fastq", 4186034926.0, 28391200.0, "GSM7017321 r4", "0:27 1:120.44", "A:1196632989;C:902024293;G:948466916;T:1135493790;N:3416938", 27, 120, null, null, 1196632989, 902024293, 948466916, 1135493790, 3416938, "SRX19235638", "SRS16640045", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00168, 0.91524, 0.00079, 0.16779, 0.9973, 0.86216, 0.37714, 0.50128, 27, 121, "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"], [74000, "SRR23292552", "SRX19235637", "SRS16640044", "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 3dSHAM Blue scRNAseq", "GSM7017320", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 3dSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017320", "GSM7017320: Sox10Cre BtR IOM 3dSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017320 r1", "GSM7017320", "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_3dSHAM_BFP-1_S21_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_BFP-1_S21_L001_R2_001.fastq.gz", "fastq fastq", 10154514668.0, 68864315.0, "GSM7017320 r1", "0:27 1:120.46", "A:2870442724;C:2220398180;G:2279010800;T:2776430093;N:8232871", 27, 120, null, null, 2870442724, 2220398180, 2279010800, 2776430093, 8232871, "SRX19235637", "SRS16640044", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00221, 0.91003, 0.00096, 0.14128, 0.99669, 0.85267, 0.49173, 0.57021, 27, 121, "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"], [74001, "SRR23292553", "SRX19235637", "SRS16640044", "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 3dSHAM Blue scRNAseq", "GSM7017320", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 3dSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017320", "GSM7017320: Sox10Cre BtR IOM 3dSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017320 r1", "GSM7017320", "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_3dSHAM_BFP-2_S22_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_BFP-2_S22_L001_R2_001.fastq.gz", "fastq fastq", 4235306292.0, 28720740.0, "GSM7017320 r2", "0:27 1:120.47", "A:1198775435;C:923216509;G:944039864;T:1165787379;N:3487105", 27, 120, null, null, 1198775435, 923216509, 944039864, 1165787379, 3487105, "SRX19235637", "SRS16640044", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00227, 0.91051, 0.00102, 0.14411, 0.99644, 0.85443, 0.48559, 0.55081, 27, 121, "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"], [74002, "SRR23292554", "SRX19235637", "SRS16640044", "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 3dSHAM Blue scRNAseq", "GSM7017320", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 3dSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017320", "GSM7017320: Sox10Cre BtR IOM 3dSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017320 r1", "GSM7017320", "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_3dSHAM_BFP-3_S23_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_BFP-3_S23_L001_R2_001.fastq.gz", "fastq fastq", 6819643924.0, 46246079.0, "GSM7017320 r3", "0:27 1:120.46", "A:1925906277;C:1494822982;G:1527609169;T:1865719001;N:5586495", 27, 120, null, null, 1925906277, 1494822982, 1527609169, 1865719001, 5586495, "SRX19235637", "SRS16640044", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00199, 0.9108, 0.0008, 0.14267, 0.99687, 0.85906, 0.43171, 0.58181, 27, 121, "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"], [74003, "SRR23292555", "SRX19235637", "SRS16640044", "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 3dSHAM Blue scRNAseq", "GSM7017320", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 3dSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017320", "GSM7017320: Sox10Cre BtR IOM 3dSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017320 r1", "GSM7017320", "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_3dSHAM_BFP-4_S24_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_3dSHAM_BFP-4_S24_L001_R2_001.fastq.gz", "fastq fastq", 6725978963.0, 45606148.0, "GSM7017320 r4", "0:27 1:120.48", "A:1898396528;C:1469917804;G:1498695962;T:1853480856;N:5487813", 27, 120, null, null, 1898396528, 1469917804, 1498695962, 1853480856, 5487813, "SRX19235637", "SRS16640044", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00211, 0.91147, 0.00092, 0.14434, 0.99685, 0.86586, 0.46086, 0.57758, 27, 121, "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"], [74004, "SRR23292556", "SRX19235636", "SRS16640043", "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 24hSHAM Red scRNAseq", "GSM7017319", 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:SHAM injury", "Sox10Cre BtR IOM 24hSHAM 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:SHAM injury", "GSM7017319", "GSM7017319: Sox10Cre BtR IOM 24hSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017319 r1", "GSM7017319", "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_24hSHAM_Red-1_S29_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Red-1_S29_L001_R2_001.fastq.gz", "fastq fastq", 128268872.0, 870430.0, "GSM7017319 r1", "0:27 1:120.36", "A:37626357;C:26184518;G:28942721;T:35299155;N:216121", 27, 120, null, null, 37626357, 26184518, 28942721, 35299155, 216121, "SRX19235636", "SRS16640043", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00211, 0.92998, 0.00077, 0.15834, 0.99715, 0.86216, 0.524, 0.56953, 27, 121, "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"], [74005, "SRR23292557", "SRX19235636", "SRS16640043", "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 24hSHAM Red scRNAseq", "GSM7017319", 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:SHAM injury", "Sox10Cre BtR IOM 24hSHAM 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:SHAM injury", "GSM7017319", "GSM7017319: Sox10Cre BtR IOM 24hSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017319 r1", "GSM7017319", "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_24hSHAM_Red-2_S30_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Red-2_S30_L001_R2_001.fastq.gz", "fastq fastq", 243379168.0, 1651445.0, "GSM7017319 r2", "0:27 1:120.37", "A:71264416;C:49792275;G:55074107;T:66839486;N:408884", 27, 120, null, null, 71264416, 49792275, 55074107, 66839486, 408884, "SRX19235636", "SRS16640043", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00228, 0.93124, 0.00097, 0.15866, 0.99728, 0.85983, 0.5909, 0.56822, 27, 120, "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"], [74006, "SRR23292558", "SRX19235636", "SRS16640043", "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 24hSHAM Red scRNAseq", "GSM7017319", 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:SHAM injury", "Sox10Cre BtR IOM 24hSHAM 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:SHAM injury", "GSM7017319", "GSM7017319: Sox10Cre BtR IOM 24hSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017319 r1", "GSM7017319", "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_24hSHAM_Red-3_S31_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Red-3_S31_L001_R2_001.fastq.gz", "fastq fastq", 214807953.0, 1457378.0, "GSM7017319 r3", "0:27 1:120.39", "A:62498451;C:43914775;G:49136468;T:58887170;N:371089", 27, 120, null, null, 62498451, 43914775, 49136468, 58887170, 371089, "SRX19235636", "SRS16640043", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00211, 0.93084, 0.00081, 0.15576, 0.99719, 0.86397, 0.54356, 0.57327, 27, 120, "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"], [74007, "SRR23292559", "SRX19235636", "SRS16640043", "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 24hSHAM Red scRNAseq", "GSM7017319", 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:SHAM injury", "Sox10Cre BtR IOM 24hSHAM 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:SHAM injury", "GSM7017319", "GSM7017319: Sox10Cre BtR IOM 24hSHAM Red scRNAseq; Danio rerio; RNA Seq", "GSM7017319 r1", "GSM7017319", "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_24hSHAM_Red-4_S32_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Red-4_S32_L001_R2_001.fastq.gz", "fastq fastq", 250394780.0, 1698902.0, "GSM7017319 r4", "0:27 1:120.39", "A:73392717;C:51210134;G:56693446;T:68677211;N:421272", 27, 120, null, null, 73392717, 51210134, 56693446, 68677211, 421272, "SRX19235636", "SRS16640043", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00225, 0.92961, 0.00091, 0.15713, 0.99711, 0.86082, 0.55421, 0.57772, 27, 120, "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"], [74008, "SRR23292560", "SRX19235635", "SRS16640042", "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 24hSHAM Blue scRNAseq", "GSM7017318", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 24hSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017318", "GSM7017318: Sox10Cre BtR IOM 24hSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017318 r1", "GSM7017318", "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_24hSHAM_Blue-1_S25_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Blue-1_S25_L001_R2_001.fastq.gz", "fastq fastq", 7154805011.0, 48527379.0, "GSM7017318 r1", "0:27 1:120.44", "A:2073479879;C:1488985362;G:1643799144;T:1936302735;N:12237891", 27, 120, null, null, 2073479879, 1488985362, 1643799144, 1936302735, 12237891, "SRX19235635", "SRS16640042", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00381, 0.9068, 0.00132, 0.13058, 0.99484, 0.84177, 0.53796, 0.54309, 27, 120, "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"], [74009, "SRR23292561", "SRX19235635", "SRS16640042", "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 24hSHAM Blue scRNAseq", "GSM7017318", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 24hSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017318", "GSM7017318: Sox10Cre BtR IOM 24hSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017318 r1", "GSM7017318", "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_24hSHAM_Blue-2_S26_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Blue-2_S26_L001_R2_001.fastq.gz", "fastq fastq", 3857895166.0, 26164218.0, "GSM7017318 r2", "0:27 1:120.45", "A:1120786431;C:797531451;G:882256326;T:1050786517;N:6534441", 27, 120, null, null, 1120786431, 797531451, 882256326, 1050786517, 6534441, "SRX19235635", "SRS16640042", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.0033, 0.90801, 0.00118, 0.13198, 0.99492, 0.83392, 0.56234, 0.54611, 27, 121, "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"], [74010, "SRR23292562", "SRX19235635", "SRS16640042", "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 24hSHAM Blue scRNAseq", "GSM7017318", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 24hSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017318", "GSM7017318: Sox10Cre BtR IOM 24hSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017318 r1", "GSM7017318", "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_24hSHAM_Blue-3_S27_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Blue-3_S27_L001_R2_001.fastq.gz", "fastq fastq", 4163888539.0, 28239751.0, "GSM7017318 r3", "0:27 1:120.45", "A:1207480915;C:863617971;G:953570955;T:1132123796;N:7094902", 27, 120, null, null, 1207480915, 863617971, 953570955, 1132123796, 7094902, "SRX19235635", "SRS16640042", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00352, 0.90726, 0.00115, 0.13006, 0.99452, 0.83749, 0.50454, 0.54893, 27, 121, "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"], [74011, "SRR23292563", "SRX19235635", "SRS16640042", "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 24hSHAM Blue scRNAseq", "GSM7017318", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "Sox10Cre BtR IOM 24hSHAM Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:SHAM injury", "GSM7017318", "GSM7017318: Sox10Cre BtR IOM 24hSHAM Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017318 r1", "GSM7017318", "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_24hSHAM_Blue-4_S28_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_24hSHAM_Blue-4_S28_L001_R2_001.fastq.gz", "fastq fastq", 3564982610.0, 24177650.0, "GSM7017318 r4", "0:27 1:120.45", "A:1031778867;C:739190723;G:819791542;T:968154217;N:6067261", 27, 120, null, null, 1031778867, 739190723, 819791542, 968154217, 6067261, "SRX19235635", "SRS16640042", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00343, 0.90741, 0.00121, 0.13101, 0.99521, 0.83853, 0.523, 0.54754, 27, 120, "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"], [74012, "SRR23292564", "SRX19235634", "SRS16640041", "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 uninjured Red scRNAseq", "GSM7017317", 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:uninjured", "Sox10Cre BtR IOM uninjured 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:uninjured", "GSM7017317", "GSM7017317: Sox10Cre BtR IOM uninjured Red scRNAseq; Danio rerio; RNA Seq", "GSM7017317 r1", "GSM7017317", "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_uninjured_Red-1_S21_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Red-1_S21_L001_R2_001.fastq.gz", "fastq fastq", 524013540.0, 3554418.0, "GSM7017317 r1", "0:27 1:120.43", "A:152678800;C:106909147;G:119162644;T:144375960;N:886989", 27, 120, null, null, 152678800, 106909147, 119162644, 144375960, 886989, "SRX19235634", "SRS16640041", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00213, 0.92296, 0.00091, 0.1594, 0.99657, 0.84587, 0.45851, 0.51072, 27, 120, "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"], [74013, "SRR23292565", "SRX19235634", "SRS16640041", "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 uninjured Red scRNAseq", "GSM7017317", 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:uninjured", "Sox10Cre BtR IOM uninjured 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:uninjured", "GSM7017317", "GSM7017317: Sox10Cre BtR IOM uninjured Red scRNAseq; Danio rerio; RNA Seq", "GSM7017317 r1", "GSM7017317", "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_uninjured_Red-2_S22_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Red-2_S22_L001_R2_001.fastq.gz", "fastq fastq", 308557013.0, 2092998.0, "GSM7017317 r2", "0:27 1:120.42", "A:90896376;C:62673340;G:69348823;T:85122937;N:515537", 27, 120, null, null, 90896376, 62673340, 69348823, 85122937, 515537, "SRX19235634", "SRS16640041", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00179, 0.9235, 0.00079, 0.15939, 0.99726, 0.84429, 0.54891, 0.52947, 27, 121, "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"], [74014, "SRR23292566", "SRX19235634", "SRS16640041", "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 uninjured Red scRNAseq", "GSM7017317", 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:uninjured", "Sox10Cre BtR IOM uninjured 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:uninjured", "GSM7017317", "GSM7017317: Sox10Cre BtR IOM uninjured Red scRNAseq; Danio rerio; RNA Seq", "GSM7017317 r1", "GSM7017317", "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_uninjured_Red-3_S23_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Red-3_S23_L001_R2_001.fastq.gz", "fastq fastq", 416908068.0, 2827836.0, "GSM7017317 r3", "0:27 1:120.43", "A:121165399;C:85074652;G:95182740;T:114787239;N:698038", 27, 120, null, null, 121165399, 85074652, 95182740, 114787239, 698038, "SRX19235634", "SRS16640041", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00199, 0.92471, 0.00082, 0.15593, 0.99703, 0.84451, 0.46788, 0.54644, 27, 121, "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"], [74015, "SRR23292567", "SRX19235634", "SRS16640041", "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 uninjured Red scRNAseq", "GSM7017317", 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:uninjured", "Sox10Cre BtR IOM uninjured 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:uninjured", "GSM7017317", "GSM7017317: Sox10Cre BtR IOM uninjured Red scRNAseq; Danio rerio; RNA Seq", "GSM7017317 r1", "GSM7017317", "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_uninjured_Red-4_S24_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Red-4_S24_L001_R2_001.fastq.gz", "fastq fastq", 344252957.0, 2335043.0, "GSM7017317 r4", "0:27 1:120.43", "A:100217268;C:70122270;G:78414300;T:94927814;N:571305", 27, 120, null, null, 100217268, 70122270, 78414300, 94927814, 571305, "SRX19235634", "SRS16640041", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00218, 0.92354, 0.00087, 0.16122, 0.99663, 0.84555, 0.53112, 0.54065, 27, 120, "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"], [74016, "SRR23292568", "SRX19235633", "SRS16640040", "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 uninjured Blue scRNAseq", "GSM7017316", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "Sox10Cre BtR IOM uninjured Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "GSM7017316", "GSM7017316: Sox10Cre BtR IOM uninjured Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017316 r1", "GSM7017316", "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_uninjured_Blue-1_S17_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Blue-1_S17_L001_R2_001.fastq.gz", "fastq fastq", 3250189695.0, 22041593.0, "GSM7017316 r1", "0:27 1:120.46", "A:948275755;C:664834970;G:737670315;T:893902390;N:5506265", 27, 120, null, null, 948275755, 664834970, 737670315, 893902390, 5506265, "SRX19235633", "SRS16640040", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00314, 0.90022, 0.00107, 0.13712, 0.99521, 0.84366, 0.5538, 0.56756, 27, 121, "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"], [74017, "SRR23292569", "SRX19235633", "SRS16640040", "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 uninjured Blue scRNAseq", "GSM7017316", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "Sox10Cre BtR IOM uninjured Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "GSM7017316", "GSM7017316: Sox10Cre BtR IOM uninjured Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017316 r1", "GSM7017316", "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_uninjured_Blue-2_S18_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Blue-2_S18_L001_R2_001.fastq.gz", "fastq fastq", 3087693444.0, 20939596.0, "GSM7017316 r2", "0:27 1:120.46", "A:900192508;C:633181367;G:700948531;T:848139097;N:5231941", 27, 120, null, null, 900192508, 633181367, 700948531, 848139097, 5231941, "SRX19235633", "SRS16640040", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.0032, 0.90046, 0.00123, 0.13574, 0.99517, 0.84333, 0.51639, 0.56162, 27, 121, "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"], [74018, "SRR23292570", "SRX19235633", "SRS16640040", "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 uninjured Blue scRNAseq", "GSM7017316", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "Sox10Cre BtR IOM uninjured Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "GSM7017316", "GSM7017316: Sox10Cre BtR IOM uninjured Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017316 r1", "GSM7017316", "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_uninjured_Blue-3_S19_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Blue-3_S19_L001_R2_001.fastq.gz", "fastq fastq", 2358180154.0, 15992521.0, "GSM7017316 r3", "0:27 1:120.46", "A:687257771;C:483050213;G:535581658;T:648302379;N:3988133", 27, 120, null, null, 687257771, 483050213, 535581658, 648302379, 3988133, "SRX19235633", "SRS16640040", "SRA1583003", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", "Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center", 2, 0.00344, 0.90064, 0.00117, 0.13551, 0.9949, 0.84236, 0.51543, 0.56675, 27, 120, "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"], [74019, "SRR23292571", "SRX19235633", "SRS16640040", "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 uninjured Blue scRNAseq", "GSM7017316", null, "source name:jaw joint|tissue:jaw joint|age:3 5mpf adult|cell type:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "Sox10Cre BtR IOM uninjured Blue 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:no enrichment|genotype:Sox10:Cre;actb2:loxP BFP STOP loxP DsRed|treatment:uninjured", "GSM7017316", "GSM7017316: Sox10Cre BtR IOM uninjured Blue scRNAseq; Danio rerio; RNA Seq", "GSM7017316 r1", "GSM7017316", "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. 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