run_metadata: 67334
This data as json
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| 67334 | SRR17117616 | SRX13302159 | SRS11213384 | SRP349128 | PRJNA785890 | Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish | GSE190115 | Transcriptome Analysis | To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs deciphered transcriptional changes and intermediate cell states during regeneration and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration | pubmed:37021774 | WT day x 1 | GSM5714327 | tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0 | WT day x 1 | Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment annotation and counting were performed using CellRanger Downstream QC Dimenstion Reduction UMAP generation and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects | Tgmitfa:nlsEGFP FACS enriched cells | 750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes | Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit | Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age | genotype:WT|day:0 | GSM5714327 | GSM5714327: WT day x 1; Danio rerio; RNA Seq | GSM5714327 r1 | GSM5714327 | 1 | Scales were removed zebrafish skin cut and peeled off underlying musce enzymatic and mechanical dissociation and mitfa:nlsEGFP cells were enriched for during FACS single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP349128 | assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate | WTD0A_possorted_genome_bam.bam | 10X Genomics bam file | 7628491300.0 | 152569826.0 | GSM5714327 r1 | 0:50 | A:2377995758;C:1521202402;G:1696947530;T:2030231260;N:2114350 | 50 | 2377995758 | 1521202402 | 1696947530 | 2030231260 | 2114350 | SRX13302159 | SRS11213384 | SRA1620868 | Craig Ceol, Molecular Medicine, UMass Medical School | Craig Ceol, Molecular Medicine, UMass Medical School | 1 | 0.90188 | 0.1668 | 0.82154 | 0.599 | 50 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-03 | Adult | Adult | Skin | Surface Structure |