|
| Status |
Public on Feb 02, 2023 |
| Title |
8wpw1_Ctrl1_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Lrig1 GL Sca1+ epidermal cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lrig1 GL Sca1+ epidermal cells
genotype: Lrig1CreER/Rosa-TdTomato
treatment: none
time: 8w pw1
region: Ctrl (non-memory) region
|
| Growth protocol |
Lrig1 GL Sca1+ cells were FACS sorted and cultured in keratinocytes complete media for 1 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Smart-Seq2 protocol
For extracted RNA, indexed cDNA libraries were obtained following the NexteraXT Illumina protocol
minibulk RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
Minibulk_Q_8wpw1_CTRL1_4
|
| Data processing |
Reads were next aligned to the mouse reference genome (UCSC mm10/GRCm38) using HiSat2 v2.2.01
Gene expression levels were quantified with featureCounts v1.6.12 (options: -t exon -g gene_name) using the GENCODE (https://www.gencodegenes.org) release M20 annotation
Gene expression counts of each cell population were next analysed using the edgeR3 R/Bioconductor package
Assembly: mm10
Supplementary files format and content: rawcounts
|
| |
|
| Submission date |
Dec 20, 2022 |
| Last update date |
Feb 02, 2023 |
| Contact name |
Andrea Lauria |
| E-mail(s) |
andrea.lauria@unito.it
|
| Organization name |
University of Turin
|
| Department |
Life Sciences and Systems Biology
|
| Lab |
Functional Genomics, Epigenomics - S. Oliviero
|
| Street address |
Via Accademia Albertina, 13
|
| City |
Turin |
| ZIP/Postal code |
10123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL32159 |
| Series (2) |
| GSE197590 |
Wound memory of epidermal stem cells |
| GSE221403 |
Lifelong tissue memory relies on spatially organized dedicated progenitors located distally from the injury [bulkRNAseq] |
|
| Relations |
| BioSample |
SAMN32329593 |
| SRA |
SRX18786904 |
