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| Status |
Public on Jul 05, 2022 |
| Title |
Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To unravel the molecular heterogeneity and characterise cell states of LRC/Non-LRC domains in interfollicular epidermis in vivo
Methods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells as H2BGFP LRCs, mid-LRCs, and non-LRCs from K5-tTA x pTRE-H2BGFP mice. Single-cell suspension from back (2-week chase) and tail skin (3-week chase) was processed for the barcoded single-cell 3′ cDNA libraries generation using Chromium Single Cell 3′ gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained.
Results: We obtained a total of 13484 and 14884 high quality cells from two different skin types after combining two datasets each from LRCs/mid-LRCs/Non-LRCs for further analysis by Seurat workflow
Conclusions: Obtained high quality single cell transcriptomic data to dissect molecular and proliferative heterogeneity of interfollicular epidermis (IFE)
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| Overall design |
Single cell RNA-seq profiles of sorted IFE LRC/Non-LRC domains from back and tail skin of wild type (WT) mice
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| Contributor(s) |
Tudorita T, Sangeeta G |
| Citation(s) |
35949182, 38934416 |
| |
| Submission date |
Jun 09, 2022 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Sangeeta Ghuwalewala |
| E-mail(s) |
[email protected]
|
| Phone |
6072796894
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Tudorita Tumbar
|
| Street address |
107 Biotechology Building 526 Campus Road
|
| City |
ITHACA |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE205746 |
Epidermal basal domains organization highlights skin robustness to environmental exposure. |
|
| Relations |
| BioProject |
PRJNA847425 |
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