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| Status |
Public on Jul 05, 2022 |
| Title |
Epidermal basal domains organization highlights skin robustness to environmental exposure [bulk RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: To unravel the molecular heterogeneity of distinct epidermal populations in interfollicular epidermis (IFE) in vivo
Methods: We performed bulk RNA sequencing of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells enriched in Slc1a3/Dlx1/Aspm CreER marked lineages. We used >10000 tdTomato+/Sca1+/α6-int+ (basal) cells from both back and tail skin at 2-weeks post TM induction from each of four CreER mouse lines and normalized them to Sca1+/α6-int+ sorted from the same mouse. Extracted RNA of high quality and low input was processed for library preparation followed by Illumina seq on HiSeq4000. The raw sample-specific FASTQ files were trimmed and mapped to the reference genome/transcriptome (mouse/mm10) and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.
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| Overall design |
Comparative gene expression profiling analysis of RNA-seq data for Slc1a3/Dlx1/Aspm basal lineages in IFE
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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
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| 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 (28)
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| This SubSeries is part of SuperSeries: |
| GSE205746 |
Epidermal basal domains organization highlights skin robustness to environmental exposure. |
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| Relations |
| BioProject |
PRJNA847426 |
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