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