|
| Status |
Public on Jul 05, 2022 |
| Title |
K14.F.BS.P5.R1 |
| Sample type |
SRA |
| |
|
| Source name |
Skin Tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skin Tissue
cell type: Back Skin Total IFE
genotype: WT(K14CreER x RosatdTomato)
treatment: 2-week post tamoxifen injection
time: PD49-Telogen
|
| Treatment protocol |
Mice at PD30-34 were injected with tamoxifen 100ug/ml for five consecutive days and harvested after 2 weeks at PD49 (telogen)
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol (Thermo Fisher) according to the manufacture's protocol. Poly A+RNA was isolated with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs).
Since our RNA was low input (<20 nt total RNA), truSeq-barcoded RNAseq libraries were generated with the Ultra II RNA Library Prep Kit (non-directional) (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were sequenced on an Illumina instrument (Hiseq4000). 2x150 bp HiSeq reads were generated with a depth of 20M.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC ;unwanted reads were removed with STAR v 2.7.0e
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression
PCA was performed on the raw counts for the different tdTomato + sorted populations normalized in both back and tail skin with their respective BL (integrin/+Sca1+) sorted control and the scores were represented in a three-dimensional scatter plot.
Assembly: mm10/mouse
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 09, 2022 |
| Last update date |
Jul 05, 2022 |
| 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 |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE205744 |
Epidermal basal domains organization highlights skin robustness to environmental exposure [bulk RNA-seq] |
| GSE205746 |
Epidermal basal domains organization highlights skin robustness to environmental exposure. |
|
| Relations |
| BioSample |
SAMN28934358 |
| SRA |
SRX15644923 |
