metadata: run_metadata: 83 rows where devstage_curation_coarse = "Adult" and tissue

83 rows where devstage_curation_coarse = "Adult" and tissue_curation = "Jaw"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34294	34294	SRR31642040	SRX27005496	SRS23470018	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.		Jaw joint cells 70 dpjr Single	GSM8671781	source name:Jaw joint\|tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2\|geo loc name:missing\|collection date:missing	Jaw joint cells 70 dpjr Single	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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2	GSM8671781	GSM8671781: Jaw joint cells 70 dpjr Single; Danio rerio; RNA Seq	GSM8671781 r1	GSM8671781	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	70dpjr_Single_Animal_L002_I1_001.fastq.gz 70dpjr_Single_Animal_L002_I2_001.fastq.gz 70dpjr_Single_Animal_L002_R1_001.fastq.gz 70dpjr_Single_Animal_L002_R2_001.fastq.gz	fastq fastq fastq fastq	37049181954.0	166888207.0	GSM8671781 r1	0:10 1:10 2:101 3:101	A:9816927833;C:6602658028;G:6479430305;T:10811804702;N:596946	10	10	101	101	9816927833	6602658028	6479430305	10811804702	596946	SRX27005496	SRS23470018	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34295	34295	SRR31642041	SRX27005496	SRS23470018	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.		Jaw joint cells 70 dpjr Single	GSM8671781	source name:Jaw joint\|tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2\|geo loc name:missing\|collection date:missing	Jaw joint cells 70 dpjr Single	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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2	GSM8671781	GSM8671781: Jaw joint cells 70 dpjr Single; Danio rerio; RNA Seq	GSM8671781 r1	GSM8671781	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	70dpjr_Single_Animal_L003_I1_001.fastq.gz 70dpjr_Single_Animal_L003_I2_001.fastq.gz 70dpjr_Single_Animal_L003_R1_001.fastq.gz 70dpjr_Single_Animal_L003_R2_001.fastq.gz	fastq fastq fastq fastq	37422563532.0	168570106.0	GSM8671781 r2	0:10 1:10 2:101 3:101	A:9984119286;C:6706845163;G:6549173156;T:10810402697;N:621110	10	10	101	101	9984119286	6706845163	6549173156	10810402697	621110	SRX27005496	SRS23470018	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34296	34296	SRR31642042	SRX27005495	SRS23470017	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.		Jaw joint cells 70 dpjr Pooled	GSM8671780	source name:Jaw joint\|tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2\|geo loc name:missing\|collection date:missing	Jaw joint cells 70 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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2	GSM8671780	GSM8671780: Jaw joint cells 70 dpjr Pooled; Danio rerio; RNA Seq	GSM8671780 r1	GSM8671780	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	70dpjr_Pooled_L002_I1_001.fastq.gz 70dpjr_Pooled_L002_I2_001.fastq.gz 70dpjr_Pooled_L002_R1_001.fastq.gz 70dpjr_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	38777301438.0	174672529.0	GSM8671780 r1	0:10 1:10 2:101 3:101	A:10225368778;C:6854296513;G:6738650656;T:11464913181;N:621730	10	10	101	101	10225368778	6854296513	6738650656	11464913181	621730	SRX27005495	SRS23470017	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34297	34297	SRR31642043	SRX27005495	SRS23470017	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.		Jaw joint cells 70 dpjr Pooled	GSM8671780	source name:Jaw joint\|tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2\|geo loc name:missing\|collection date:missing	Jaw joint cells 70 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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:70 dpjr\|batch:2	GSM8671780	GSM8671780: Jaw joint cells 70 dpjr Pooled; Danio rerio; RNA Seq	GSM8671780 r1	GSM8671780	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	70dpjr_Pooled_L003_I1_001.fastq.gz 70dpjr_Pooled_L003_I2_001.fastq.gz 70dpjr_Pooled_L003_R1_001.fastq.gz 70dpjr_Pooled_L003_R2_001.fastq.gz	fastq fastq fastq fastq	39504660018.0	177948919.0	GSM8671780 r2	0:10 1:10 2:101 3:101	A:10484112013;C:7025634996;G:6867358428;T:11567917628;N:658573	10	10	101	101	10484112013	7025634996	6867358428	11567917628	658573	SRX27005495	SRS23470017	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34298	34298	SRR31642044	SRX27005494	SRS23470016	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.		Jaw joint cells 28 dpjr Single Animal	GSM8671779	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 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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:28 dpjr\|batch:2	GSM8671779	GSM8671779: Jaw joint cells 28 dpjr Single Animal; Danio rerio; RNA Seq	GSM8671779 r1	GSM8671779	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	28dpjr_Single_Animal_L002_I1_001.fastq.gz 28dpjr_Single_Animal_L002_I2_001.fastq.gz 28dpjr_Single_Animal_L002_R1_001.fastq.gz 28dpjr_Single_Animal_L002_R2_001.fastq.gz	fastq fastq fastq fastq	36462195750.0	164244125.0	GSM8671779 r1	0:10 1:10 2:101 3:101	A:9480759740;C:6602174265;G:6480198740;T:10613598349;N:582156	10	10	101	101	9480759740	6602174265	6480198740	10613598349	582156	SRX27005494	SRS23470016	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34299	34299	SRR31642045	SRX27005494	SRS23470016	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.		Jaw joint cells 28 dpjr Single Animal	GSM8671779	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 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′ 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.	tissue:Jaw joint\|genotype:Sox10Cre;actb2:loxP BFP loxP DsRed; flk1:GFP\|age:3 mpf 6 mpf\|treatment:28 dpjr\|batch:2	GSM8671779	GSM8671779: Jaw joint cells 28 dpjr Single Animal; Danio rerio; RNA Seq	GSM8671779 r1	GSM8671779	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	28dpjr_Single_Animal_L003_I1_001.fastq.gz 28dpjr_Single_Animal_L003_I2_001.fastq.gz 28dpjr_Single_Animal_L003_R1_001.fastq.gz 28dpjr_Single_Animal_L003_R2_001.fastq.gz	fastq fastq fastq fastq	37308768774.0	168057517.0	GSM8671779 r2	0:10 1:10 2:101 3:101	A:9765937139;C:6796393106;G:6628239898;T:10756427871;N:620420	10	10	101	101	9765937139	6796393106	6628239898	10756427871	620420	SRX27005494	SRS23470016	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34300	34300	SRR31642046	SRX27005493	SRS23470015	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.		Jaw joint cells 28 dpjr Pooled	GSM8671778	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	28dpjr_Pooled_L002_I1_001.fastq.gz 28dpjr_Pooled_L002_I2_001.fastq.gz 28dpjr_Pooled_L002_R1_001.fastq.gz 28dpjr_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	37406314908.0	168496914.0	GSM8671778 r1	0:10 1:10 2:101 3:101	A:9851624515;C:6742015789;G:6561704544;T:10880437218;N:594562	10	10	101	101	9851624515	6742015789	6561704544	10880437218	594562	SRX27005493	SRS23470015	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34301	34301	SRR31642047	SRX27005493	SRS23470015	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.		Jaw joint cells 28 dpjr Pooled	GSM8671778	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	28dpjr_Pooled_L003_I1_001.fastq.gz 28dpjr_Pooled_L003_I2_001.fastq.gz 28dpjr_Pooled_L003_R1_001.fastq.gz 28dpjr_Pooled_L003_R2_001.fastq.gz	fastq fastq fastq fastq	38288256750.0	172469625.0	GSM8671778 r2	0:10 1:10 2:101 3:101	A:10150332803;C:6940223173;G:6717128076;T:11030541750;N:638448	10	10	101	101	10150332803	6940223173	6717128076	11030541750	638448	SRX27005493	SRS23470015	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34302	34302	SRR31642048	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.		Jaw joint cells 14 dpjr Single Animal	GSM8671777	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	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												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34303	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.		Jaw joint cells 14 dpjr Single Animal	GSM8671777	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	14dpjr_Single_Animal_L003_I1_001.fastq.gz 14dpjr_Single_Animal_L003_I2_001.fastq.gz 14dpjr_Single_Animal_L003_R1_001.fastq.gz 14dpjr_Single_Animal_L003_R2_001.fastq.gz	fastq fastq fastq fastq	37643417790.0	169564945.0	GSM8671777 r2	0:10 1:10 2:101 3:101	A:9871564441;C:7084478503;G:6791319850;T:10504128919;N:627177	10	10	101	101	9871564441	7084478503	6791319850	10504128919	627177	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												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34304	34304	SRR31642050	SRX27005491	SRS23470013	SRP550052	PRJNA1195551	scRNAseq gene expression profile of zebrafish jaw joint cells post complete resection of the synovial jaw joint	GSE283763	Transcriptome Analysis	Adult mammalian synovial joints have limited regenerative capacity where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single cell RNA sequencing we profile RNA expression from live sorted jaw joint cells throughout the time course of joint regeneration 1 to 70 days post joint resection dpjr. Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage. Overall design: scRNAseq was performed on live sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post joint resection 1 3 7 14 28 and 70 dpjr to capture the major stages of healing post resection.		Jaw joint cells 14 dpjr Pooled	GSM8671776	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	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												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34305	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.		Jaw joint cells 14 dpjr Pooled	GSM8671776	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	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												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34306	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.		Jaw joint cells 7 dpjr Single Animal	GSM8671775	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	7dpjr_Single_Animal_L001_I1_001.fastq.gz 7dpjr_Single_Animal_L001_I2_001.fastq.gz 7dpjr_Single_Animal_L001_R1_001.fastq.gz 7dpjr_Single_Animal_L001_R2_001.fastq.gz	fastq fastq fastq fastq	40902096516.0	184243678.0	GSM8671775 r1	0:10 1:10 2:101 3:101	A:9783975092;C:6823114397;G:6613251892;T:13996577499;N:304076	10	10	101	101	9783975092	6823114397	6613251892	13996577499	304076	SRX27005490	SRS23470012	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34307	34307	SRR31642053	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.		Jaw joint cells 7 dpjr Single Animal	GSM8671775	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′ 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.	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′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	7dpjr_Single_Animal_L002_I1_001.fastq.gz 7dpjr_Single_Animal_L002_I2_001.fastq.gz 7dpjr_Single_Animal_L002_R1_001.fastq.gz 7dpjr_Single_Animal_L002_R2_001.fastq.gz	fastq fastq fastq fastq	41355254682.0	186284931.0	GSM8671775 r2	0:10 1:10 2:101 3:101	A:9943607268;C:6874125553;G:6628853095;T:14182629385;N:340761	10	10	101	101	9943607268	6874125553	6628853095	14182629385	340761	SRX27005490	SRS23470012	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34308	34308	SRR31642054	SRX27005489	SRS23470011	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.		Jaw joint cells 7 dpjr Pooled	GSM8671774	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	7dpjr_Pooled_L001_I1_001.fastq.gz 7dpjr_Pooled_L001_I2_001.fastq.gz 7dpjr_Pooled_L001_R1_001.fastq.gz 7dpjr_Pooled_L001_R2_001.fastq.gz	fastq fastq fastq fastq	53197411338.0	239627979.0	GSM8671774 r1	0:10 1:10 2:101 3:101	A:12697683552;C:8693291955;G:8466190901;T:18547291431;N:393919	10	10	101	101	12697683552	8693291955	8466190901	18547291431	393919	SRX27005489	SRS23470011	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34309	34309	SRR31642055	SRX27005489	SRS23470011	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.		Jaw joint cells 7 dpjr Pooled	GSM8671774	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	7dpjr_Pooled_L002_I1_001.fastq.gz 7dpjr_Pooled_L002_I2_001.fastq.gz 7dpjr_Pooled_L002_R1_001.fastq.gz 7dpjr_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	53485697430.0	240926565.0	GSM8671774 r2	0:10 1:10 2:101 3:101	A:12829769456;C:8708244775;G:8441746450;T:18686966286;N:439163	10	10	101	101	12829769456	8708244775	8441746450	18686966286	439163	SRX27005489	SRS23470011	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34310	34310	SRR31642056	SRX27005488	SRS23470010	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.		Jaw joint cells 3 dpjr Single Animal	GSM8671773	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	3dpjr_Single_Animal_L001_I1_001.fastq.gz 3dpjr_Single_Animal_L001_I2_001.fastq.gz 3dpjr_Single_Animal_L001_R1_001.fastq.gz 3dpjr_Single_Animal_L001_R2_001.fastq.gz	fastq fastq fastq fastq	49273120002.0	221950991.0	GSM8671773 r1	0:10 1:10 2:101 3:101	A:11736989822;C:8276159891;G:8014521470;T:16806059958;N:369041	10	10	101	101	11736989822	8276159891	8014521470	16806059958	369041	SRX27005488	SRS23470010	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34311	34311	SRR31642057	SRX27005488	SRS23470010	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.		Jaw joint cells 3 dpjr Single Animal	GSM8671773	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	3dpjr_Single_Animal_L002_I1_001.fastq.gz 3dpjr_Single_Animal_L002_I2_001.fastq.gz 3dpjr_Single_Animal_L002_R1_001.fastq.gz 3dpjr_Single_Animal_L002_R2_001.fastq.gz	fastq fastq fastq fastq	49592342904.0	223388932.0	GSM8671773 r2	0:10 1:10 2:101 3:101	A:11873700952;C:8297783357;G:7995460477;T:16957208840;N:410638	10	10	101	101	11873700952	8297783357	7995460477	16957208840	410638	SRX27005488	SRS23470010	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34312	34312	SRR31642058	SRX27005487	SRS23470009	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.		Jaw joint cells 3 dpjr Pooled	GSM8671772	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	3dpjr_Pooled_L001_I1_001.fastq.gz 3dpjr_Pooled_L001_I2_001.fastq.gz 3dpjr_Pooled_L001_R1_001.fastq.gz 3dpjr_Pooled_L001_R2_001.fastq.gz	fastq fastq fastq fastq	44552263362.0	200685871.0	GSM8671772 r1	0:10 1:10 2:101 3:101	A:10490408187;C:7710053398;G:7420808306;T:14916942634;N:333417	10	10	101	101	10490408187	7710053398	7420808306	14916942634	333417	SRX27005487	SRS23470009	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34313	34313	SRR31642059	SRX27005487	SRS23470009	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.		Jaw joint cells 3 dpjr Pooled	GSM8671772	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	3dpjr_Pooled_L002_I1_001.fastq.gz 3dpjr_Pooled_L002_I2_001.fastq.gz 3dpjr_Pooled_L002_R1_001.fastq.gz 3dpjr_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	44828540142.0	201930361.0	GSM8671772 r2	0:10 1:10 2:101 3:101	A:10609297758;C:7728774755;G:7401748035;T:15049741661;N:370713	10	10	101	101	10609297758	7728774755	7401748035	15049741661	370713	SRX27005487	SRS23470009	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34314	34314	SRR31642060	SRX27005486	SRS23470008	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.		Jaw joint cells 1 dpjr Single Animal	GSM8671771	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	1dpjr_Single_Animal_L001_I1_001.fastq.gz 1dpjr_Single_Animal_L001_I2_001.fastq.gz 1dpjr_Single_Animal_L001_R1_001.fastq.gz 1dpjr_Single_Animal_L001_R2_001.fastq.gz	fastq fastq fastq fastq	42674862642.0	192229111.0	GSM8671771 r1	0:10 1:10 2:101 3:101	A:10158179078;C:7131592111;G:6936536781;T:14603653251;N:319201	10	10	101	101	10158179078	7131592111	6936536781	14603653251	319201	SRX27005486	SRS23470008	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34315	34315	SRR31642061	SRX27005486	SRS23470008	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.		Jaw joint cells 1 dpjr Single Animal	GSM8671771	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	1dpjr_Single_Animal_L002_I1_001.fastq.gz 1dpjr_Single_Animal_L002_I2_001.fastq.gz 1dpjr_Single_Animal_L002_R1_001.fastq.gz 1dpjr_Single_Animal_L002_R2_001.fastq.gz	fastq fastq fastq fastq	42871754220.0	193116010.0	GSM8671771 r2	0:10 1:10 2:101 3:101	A:10257131897;C:7136718897;G:6908261223;T:14706965739;N:356264	10	10	101	101	10257131897	7136718897	6908261223	14706965739	356264	SRX27005486	SRS23470008	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34316	34316	SRR31642062	SRX27005485	SRS23470007	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.		Jaw joint cells 1 dpjr Pooled	GSM8671770	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	1dpjr_Pooled_L001_I1_001.fastq.gz 1dpjr_Pooled_L001_I2_001.fastq.gz 1dpjr_Pooled_L001_R1_001.fastq.gz 1dpjr_Pooled_L001_R2_001.fastq.gz	fastq fastq fastq fastq	42118392336.0	189722488.0	GSM8671770 r1	0:10 1:10 2:101 3:101	A:10107137753;C:6968180312;G:6833097097;T:14415214595;N:312819	10	10	101	101	10107137753	6968180312	6833097097	14415214595	312819	SRX27005485	SRS23470007	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34317	34317	SRR31642063	SRX27005485	SRS23470007	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.		Jaw joint cells 1 dpjr Pooled	GSM8671770	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	1dpjr_Pooled_L002_I1_001.fastq.gz 1dpjr_Pooled_L002_I2_001.fastq.gz 1dpjr_Pooled_L002_R1_001.fastq.gz 1dpjr_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	42373992258.0	190873839.0	GSM8671770 r2	0:10 1:10 2:101 3:101	A:10221244303;C:6981947133;G:6814497183;T:14538473757;N:353102	10	10	101	101	10221244303	6981947133	6814497183	14538473757	353102	SRX27005485	SRS23470007	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34318	34318	SRR31642064	SRX27005484	SRS23470006	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.		Jaw joint cells Uninjured Single Animal 2	GSM8671769	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Single_Animal_2_L001_I1_001.fastq.gz Uninjured_Single_Animal_2_L001_I2_001.fastq.gz Uninjured_Single_Animal_2_L001_R1_001.fastq.gz Uninjured_Single_Animal_2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	44002559172.0	198209726.0	GSM8671769 r1	0:10 1:10 2:101 3:101	A:10399936361;C:7407718592;G:7226570159;T:15003813457;N:326083	10	10	101	101	10399936361	7407718592	7226570159	15003813457	326083	SRX27005484	SRS23470006	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34319	34319	SRR31642065	SRX27005484	SRS23470006	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.		Jaw joint cells Uninjured Single Animal 2	GSM8671769	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Single_Animal_2_L002_I1_001.fastq.gz Uninjured_Single_Animal_2_L002_I2_001.fastq.gz Uninjured_Single_Animal_2_L002_R1_001.fastq.gz Uninjured_Single_Animal_2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	44326343508.0	199668214.0	GSM8671769 r2	0:10 1:10 2:101 3:101	A:10528879457;C:7433951690;G:7216222556;T:15153558176;N:367349	10	10	101	101	10528879457	7433951690	7216222556	15153558176	367349	SRX27005484	SRS23470006	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34320	34320	SRR31642066	SRX27005483	SRS23470005	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.		Jaw joint cells Uninjured Single Animal 1	GSM8671768	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Single_Animal_1_L002_I1_001.fastq.gz Uninjured_Single_Animal_1_L002_I2_001.fastq.gz Uninjured_Single_Animal_1_L002_R1_001.fastq.gz Uninjured_Single_Animal_1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	42273543918.0	190421369.0	GSM8671768 r1	0:10 1:10 2:101 3:101	A:10987118484;C:7700883520;G:7585109100;T:12191335494;N:669940	10	10	101	101	10987118484	7700883520	7585109100	12191335494	669940	SRX27005483	SRS23470005	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34321	34321	SRR31642067	SRX27005483	SRS23470005	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.		Jaw joint cells Uninjured Single Animal 1	GSM8671768	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Single_Animal_1_L003_I1_001.fastq.gz Uninjured_Single_Animal_1_L003_I2_001.fastq.gz Uninjured_Single_Animal_1_L003_R1_001.fastq.gz Uninjured_Single_Animal_1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	43210917384.0	194643772.0	GSM8671768 r2	0:10 1:10 2:101 3:101	A:11303072754;C:7914534277;G:7759329632;T:12340392808;N:712473	10	10	101	101	11303072754	7914534277	7759329632	12340392808	712473	SRX27005483	SRS23470005	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34322	34322	SRR31642068	SRX27005482	SRS23470004	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.		Jaw joint cells Uninjured Pooled	GSM8671767	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Pooled_L001_I1_001.fastq.gz Uninjured_Pooled_L001_I2_001.fastq.gz Uninjured_Pooled_L001_R1_001.fastq.gz Uninjured_Pooled_L001_R2_001.fastq.gz	fastq fastq fastq fastq	44953034856.0	202491148.0	GSM8671767 r1	0:10 1:10 2:101 3:101	A:10830949570;C:7341800999;G:7101623323;T:15628500376;N:337628	10	10	101	101	10830949570	7341800999	7101623323	15628500376	337628	SRX27005482	SRS23470004	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
34323	34323	SRR31642069	SRX27005482	SRS23470004	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.		Jaw joint cells Uninjured Pooled	GSM8671767	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′ 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.	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. FACS was used to sort for live cells. scRNAseq libraries were prepared using the Chromium Single Cell 3′ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP550052	loader:fastq load.py	Uninjured_Pooled_L002_I1_001.fastq.gz Uninjured_Pooled_L002_I2_001.fastq.gz Uninjured_Pooled_L002_R1_001.fastq.gz Uninjured_Pooled_L002_R2_001.fastq.gz	fastq fastq fastq fastq	45169152966.0	203464653.0	GSM8671767 r2	0:10 1:10 2:101 3:101	A:10937981456;C:7348369082;G:7073920761;T:15739215927;N:372680	10	10	101	101	10937981456	7348369082	7073920761	15739215927	372680	SRX27005482	SRS23470004	SRA2029585	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-12-08	Adult	Adult	Jaw	Surface Structure
56002	56002	SRR10895909	SRX7564570	SRS6001798	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.	pubmed:33545088;pubmed:12470943		Zebrafish 003	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Jaw\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio : adult	CL100103858 L02 6	CL100103858 L02 6				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982		CL100103858_L02_524_1.fq.gz CL100103858_L02_524_2.fq.gz	fastq fastq	8863838800.0	88638388.0	CL100103858 L02 524 1.fq.gz	0:100 1:100	A:2346347928;C:2037236505;G:2089998345;T:2378150886;N:12105136	100	100			2346347928	2037236505	2089998345	2378150886	12105136	SRX7564570	SRS6001798	SRA1026516	BGI\|BGI-Research	BGI	1	0.93198		0.08128		0.74519		0.48951		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Jaw	Surface Structure
56003	56003	SRR10895910	SRX7564569	SRS6001798	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.	pubmed:33545088;pubmed:12470943		Zebrafish 003	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Jaw\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio : adult	CL100103858 L02 5	CL100103858 L02 5				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982		CL100103858_L02_521_2.fq.gz CL100103858_L02_521_1.fq.gz	fastq fastq	10301853000.0	103018530.0	CL100103858 L02 521 1.fq.gz	0:100 1:100	A:2719789797;C:2379371302;G:2435354849;T:2753122052;N:14215000	100	100			2719789797	2379371302	2435354849	2753122052	14215000	SRX7564569	SRS6001798	SRA1026516	BGI\|BGI-Research	BGI	1	0.93582		0.08016		0.73466		0.4997		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Jaw	Surface Structure
56004	56004	SRR10895911	SRX7564568	SRS6001798	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.	pubmed:33545088;pubmed:12470943		Zebrafish 003	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Jaw\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio : adult	CL100103858 L02 4	CL100103858 L02 4				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982		CL100103858_L02_522_1.fq.gz CL100103858_L02_522_2.fq.gz	fastq fastq	8856151600.0	88561516.0	CL100103858 L02 522 1.fq.gz	0:100 1:100	A:2327973616;C:2055012813;G:2104952956;T:2356113813;N:12098402	100	100			2327973616	2055012813	2104952956	2356113813	12098402	SRX7564568	SRS6001798	SRA1026516	BGI\|BGI-Research	BGI	1	0.93888		0.07312		0.74337		0.50608		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Jaw	Surface Structure
56005	56005	SRR10895912	SRX7564567	SRS6001798	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.	pubmed:33545088;pubmed:12470943		Zebrafish 003	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Jaw\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio : adult	CL100103858 L02 3	CL100103858 L02 3				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982		CL100103858_L02_525_1.fq.gz CL100103858_L02_525_2.fq.gz	fastq fastq	8393966200.0	83939662.0	CL100103858 L02 525 1.fq.gz	0:100 1:100	A:2205916604;C:1944354784;G:1992482736;T:2239434609;N:11777467	100	100			2205916604	1944354784	1992482736	2239434609	11777467	SRX7564567	SRS6001798	SRA1026516	BGI\|BGI-Research	BGI	1	0.93522		0.07124		0.73939		0.50385		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Jaw	Surface Structure
56006	56006	SRR10895914	SRX7564565	SRS6001798	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.	pubmed:33545088;pubmed:12470943		Zebrafish 003	strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Jaw\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio : adult	CL100103858 L02 2	CL100103858 L02 2				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982		CL100103858_L02_523_2.fq.gz CL100103858_L02_523_1.fq.gz	fastq fastq	9645085400.0	96450854.0	CL100103858 L02 523 1.fq.gz	0:100 1:100	A:2543300716;C:2229112849;G:2282624833;T:2576502560;N:13544442	100	100			2543300716	2229112849	2282624833	2576502560	13544442	SRX7564565	SRS6001798	SRA1026516	BGI\|BGI-Research	BGI	1	0.93673		0.0738		0.74337		0.49427		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Jaw	Surface Structure
66178	66178	SRR15964630	SRX12254437	SRS10230009	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	pubmed:35127702	trps1:eGFP enriched	GSM5587035	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		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	cell type:trps1:eGFP positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587035	GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq	GSM5587035		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:GSM5587035	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP337784		trps1enriched-1_R1_001.fastq.gz trps1enriched-1_R2_001.fastq.gz	fastq fastq	21524957734.0	145963727.0	GSM5587035 r1	0:27 1:120.47	A:6080775237;C:4508264559;G:4702878554;T:6215461741;N:17577643	27	120			6080775237	4508264559	4702878554	6215461741	17577643	SRX12254437	SRS10230009	SRA1296796	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00341	0.91093	0.00112	0.14627	0.99391	0.85693	0.46102	0.48941	27	121	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66179	66179	SRR15964631	SRX12254437	SRS10230009	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	pubmed:35127702	trps1:eGFP enriched	GSM5587035	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		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	cell type:trps1:eGFP positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587035	GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq	GSM5587035		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:GSM5587035	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP337784		trps1enriched-2_R1_001.fastq.gz trps1enriched-2_R2_001.fastq.gz	fastq fastq	29538626136.0	200298691.0	GSM5587035 r2	0:27 1:120.47	A:8358449730;C:6152852316;G:6409091874;T:8594034218;N:24197998	27	120			8358449730	6152852316	6409091874	8594034218	24197998	SRX12254437	SRS10230009	SRA1296796	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00359	0.90985	0.00119	0.14958	0.99338	0.85878	0.42675	0.48789	27	118	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66180	66180	SRR15964632	SRX12254437	SRS10230009	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	pubmed:35127702	trps1:eGFP enriched	GSM5587035	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		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	cell type:trps1:eGFP positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587035	GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq	GSM5587035		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:GSM5587035	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP337784		trps1enriched-3_R1_001.fastq.gz trps1enriched-3_R2_001.fastq.gz	fastq fastq	18834117972.0	127723979.0	GSM5587035 r3	0:27 1:120.46	A:5321823966;C:3931395608;G:4123902269;T:5441824191;N:15171938	27	120			5321823966	3931395608	4123902269	5441824191	15171938	SRX12254437	SRS10230009	SRA1296796	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00356	0.91092	0.00098	0.1444	0.99308	0.85066	0.45652	0.50535	27	121	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66181	66181	SRR15964633	SRX12254437	SRS10230009	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	pubmed:35127702	trps1:eGFP enriched	GSM5587035	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		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	cell type:trps1:eGFP positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587035	GSM5587035: trps1:eGFP enriched; Danio rerio; RNA Seq	GSM5587035		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:GSM5587035	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP337784		trps1enriched-4_R1_001.fastq.gz trps1enriched-4_R2_001.fastq.gz	fastq fastq	24543217204.0	166435205.0	GSM5587035 r4	0:27 1:120.46	A:6923484050;C:5154357751;G:5378630657;T:7066659666;N:20085080	27	120			6923484050	5154357751	5378630657	7066659666	20085080	SRX12254437	SRS10230009	SRA1296796	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00342	0.91125	0.00108	0.1445	0.99385	0.85279	0.4379	0.5084	27	121	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66182	66182	SRR15964626	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	pubmed:35127702	sox10:DsRed enriched	GSM5587034	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		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	cell type:sox10:DsRed positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587034	GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq	GSM5587034		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	SRP337784		sox10enriched-1_R1_001.fastq.gz sox10enriched-1_R2_001.fastq.gz	fastq fastq	2310039840.0	15674545.0	GSM5587034 r1	0:27 1:120.38	A:657104627;C:477823382;G:502418027;T:670802267;N:1891537	27	120			657104627	477823382	502418027	670802267	1891537	SRX12254436	SRS10230008	SRA1296796	GEO	Smeeton Lab, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center	2	0.00331	0.90804	0.00124	0.19789	0.99385	0.84918	0.5	0.4965	27	119	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66183	66183	SRR15964627	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	pubmed:35127702	sox10:DsRed enriched	GSM5587034	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		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	cell type:sox10:DsRed positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587034	GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq	GSM5587034		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	SRP337784		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			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	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66184	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	pubmed:35127702	sox10:DsRed enriched	GSM5587034	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		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	cell type:sox10:DsRed positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587034	GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq	GSM5587034		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	SRP337784		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			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	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
66185	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	pubmed:35127702	sox10:DsRed enriched	GSM5587034	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		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	cell type:sox10:DsRed positive joint cell\|age:3 mpf\|tissue:Jaw joint	GSM5587034	GSM5587034: sox10:DsRed enriched; Danio rerio; RNA Seq	GSM5587034		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	SRP337784		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			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	United States	2021-09-19	Adult	Adult	Jaw	Surface Structure
73980	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Red scRNAseq	GSM7017325	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73981	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Red scRNAseq	GSM7017325	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73982	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Red scRNAseq	GSM7017325	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73983	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Red scRNAseq	GSM7017325	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73984	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Blue scRNAseq	GSM7017324	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73985	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Blue scRNAseq	GSM7017324	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73986	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Blue scRNAseq	GSM7017324	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73987	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.	pubmed:37726321	Sox10Cre BtR IOM 3dplt Blue scRNAseq	GSM7017324	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73988	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Red scRNAseq	GSM7017323	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73989	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Red scRNAseq	GSM7017323	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73990	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Red scRNAseq	GSM7017323	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73991	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Red scRNAseq	GSM7017323	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73992	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Blue scRNAseq	GSM7017322	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73993	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Blue scRNAseq	GSM7017322	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73994	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Blue scRNAseq	GSM7017322	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73995	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.	pubmed:37726321	Sox10Cre BtR IOM 24hplt Blue scRNAseq	GSM7017322	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73996	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Red scRNAseq	GSM7017321	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73997	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Red scRNAseq	GSM7017321	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73998	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Red scRNAseq	GSM7017321	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
73999	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Red scRNAseq	GSM7017321	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74000	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Blue scRNAseq	GSM7017320	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74001	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Blue scRNAseq	GSM7017320	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74002	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Blue scRNAseq	GSM7017320	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74003	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.	pubmed:37726321	Sox10Cre BtR IOM 3dSHAM Blue scRNAseq	GSM7017320	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74004	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Red scRNAseq	GSM7017319	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74005	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Red scRNAseq	GSM7017319	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74006	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Red scRNAseq	GSM7017319	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74007	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Red scRNAseq	GSM7017319	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74008	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Blue scRNAseq	GSM7017318	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74009	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Blue scRNAseq	GSM7017318	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74010	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Blue scRNAseq	GSM7017318	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74011	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.	pubmed:37726321	Sox10Cre BtR IOM 24hSHAM Blue scRNAseq	GSM7017318	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74012	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Red scRNAseq	GSM7017317	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74013	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Red scRNAseq	GSM7017317	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74014	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Red scRNAseq	GSM7017317	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74015	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Red scRNAseq	GSM7017317	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74016	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Blue scRNAseq	GSM7017316	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74017	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Blue scRNAseq	GSM7017316	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74018	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Blue scRNAseq	GSM7017316	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		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			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	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure
74019	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.	pubmed:37726321	Sox10Cre BtR IOM uninjured Blue scRNAseq	GSM7017316	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.	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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP420343		Sox10Cre_BtR_IOM_uninjured_Blue-4_S20_L001_R1_001.fastq.gz Sox10Cre_BtR_IOM_uninjured_Blue-4_S20_L001_R2_001.fastq.gz	fastq fastq	3360985352.0	22792951.0	GSM7017316 r4	0:27 1:120.46	A:979402949;C:689485599;G:764657821;T:921760881;N:5678102	27	120			979402949	689485599	764657821	921760881	5678102	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	0.00364	0.90106	0.00156	0.135	0.99519	0.84476	0.52685	0.57087	27	121	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-01-31	Adult	Adult	Jaw	Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;