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| Status |
Public on Oct 23, 2023 |
| Title |
Unwounded Dorsal Skin scRNA-seq |
| Sample type |
SRA |
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| Source name |
Dorsal skin
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| Organism |
Mus musculus |
| Characteristics |
cell type: Dorsal skin
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were isolated from excised tissue from naïve animals (pooled from 3 wounds) using a collagenase/dispase digestion. Cells were stained with antibodies against CD45 (hematopoietic), CD31 (endothelial) and Ter119 (red blood cells); live cells were discriminated with DAPI. At least 100,000 live, CD45-CD31-Ter119- cells were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper. In brief, cells at 150,000 cells/ml, barcoded beads at 175,000 beads/ml and droplet generation oil were co-flowed at a rate of 4, 4, and 15 ml/hour, respectively, in a PDMS microfluidics chip to generate oil droplets containing beads and lysed cells. Post flow, droplets were broken and reverse transcription performed. Complementary DNA was PCR amplified, magnetically cleaned up and subjected to tagmentation and sequencing library construction. Prepared libraries were cleaned up and sequenced via Illumina HiSeq4000 or NovaSeq.
Drop-seq protocol v.3.1; uses Illumina reagents
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Data were analyzed using Partek Flow; cells with fewer than 5% mitochondrial reads were included in the analysis. tSNE and UMAP plots were created with default settings.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows
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| Submission date |
Oct 22, 2020 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Hans I-Chen Harn |
| E-mail(s) |
hharn@usc.edu
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| Organization name |
University of Southern California
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| Street address |
2011 Zonal Ave. HMR304
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE159827 |
Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration [scRNA-seq] |
| GSE159939 |
Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration |
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| Relations |
| BioSample |
SAMN16516536 |
| SRA |
SRX9341674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4848109_Unwounded.txt.gz |
12.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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