run_metadata: 66185
This data as json
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| 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 |