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| Status |
Public on Mar 26, 2024 |
| Title |
AnaVI (P32) skin mouse 2, scRNA-seq |
| Sample type |
SRA |
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| Source name |
AnaVI back skin
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| Organism |
Mus musculus |
| Characteristics |
tissue: AnaVI (P32) skin mouse 2
cell line: ---
cell type: Skin and hair follicle cells
genotype: wild-type
treatment: ---
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| Extracted molecule |
total RNA |
| Extraction protocol |
To isolate cells from mouse back skin, samples were dissected and digested in 0.25% collagenase (Sigma) in HBSS for 35 min before 0.25% trypsin-EDTA for an additional 15 min. Single cell suspensions were obtained by scraping the epidermal side gently using a blunt scalpel. After washing with FACS buffer (5% FBS in PBS), cells were filtered through 70- and 45-μm strainers, pelleted, washed with FACS buffer, and incubated with published antibodies for 20 min on ice. To resuspend autologous hair follicle stem cells (HFSCs), 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleting, washed with Cell Staining Buffer, and incubated with TotalSeq-B hashtag antibodies for 20 min on ice.
Libraries were constructed according to the manufacter’s instructions (3' Gene Expression V3, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
Sample and cell demultiplexing, alignment, filtering, barcode counting, and sample aggregation were performed using the Cell Ranger software v7.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
May 04, 2023 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Matthew T Tierney |
| E-mail(s) |
[email protected]
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| Phone |
5857974876
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| Organization name |
Rockefeller University
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| Street address |
1230 York Ave, Box 300
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE231731 |
Retinoic acid promotes tissue regeneration by resolving stem cell lineage plasticity |
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| Relations |
| BioSample |
SAMN34590102 |
| SRA |
SRX20228433 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7299725_AnaVI_2_barcodes.tsv.gz |
64.0 Kb |
(ftp)(http) |
TSV |
| GSM7299725_AnaVI_2_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM7299725_AnaVI_2_matrix.mtx.gz |
148.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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