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| Status |
Public on Jul 25, 2023 |
| Title |
UG, biological replicate 1 |
| Sample type |
SRA |
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| Source name |
Skin
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skin
cell type: Immune cells
strain: C3H/HeJ
disease state: No disease
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| Extracted molecule |
total RNA |
| Extraction protocol |
For mice, dorsal skin was isolated, subcutaneous fat was removed, and was cut into small pieces prior to digestion with 0.25% collagenase type IV in Dulbecco’s Modified Eagle Medium at 37C for 1 hour in a shaking incubator. Collagenase was neutralized with Advanced RPMI 1640 Medium + 10% FBS and the digested skin was passed through a 70um strainer. The flow through was rinsed twice with centrifugation at 350g, 4C. Single-cell suspensions were stained with anti-CD45-FITC antibody and propidium iodide. CD45+, propidium iodide- cells were isolated via FACS. For human samples, human scalp biopsies were digested using the Whole Skin Dissociation Kit and its accompanying protocol, which involved the use of a gentleMACS Dissociator. Cells were resuspended and washed in 2% FBS in Cell Staining Buffer, then stained with DRAQ5 and SYTOX-Green prior to FACS isolation for DRAQ5- SYTOX-Green- live cells.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kits (version 2 for mouse, version 3 for human samples) according to the manufacturer’s instructions, with a target of 5000 cells and 350 million reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1
Assembly: mm10, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jun 01, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Eunice Y Lee |
| Organization name |
University of California, San Francisco
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| Street address |
505 Parnassus Ave
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| City |
San Francisco |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE233906 |
Functional interrogation of lymphocyte subsets in alopecia areata using single-cell RNA sequencing |
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| Relations |
| BioSample |
SAMN35557758 |
| SRA |
SRX20567712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7438935_UG1_barcodes.tsv.gz |
16.9 Kb |
(ftp)(http) |
TSV |
| GSM7438935_UG1_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM7438935_UG1_matrix.mtx.gz |
23.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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