|
| Status |
Public on Dec 01, 2021 |
| Title |
Control_IMQ |
| Sample type |
SRA |
| |
|
| Source name |
Mouse back skin
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
treatment: IMQ
cell barcode suffix for aggr file: -2
|
| Treatment protocol |
Mice at 7~8 weeks of age received one dose of 62.5 mg 5% IMQ cream (Perrigo) on shaved backs.
|
| Growth protocol |
All mouse lines were maintained and bred following the procedures that conform with and have been approved by the UC Irvine Institutional Animal Care and Use Committee (IACUC).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3สน Reagents Kits v2 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 2.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across all the libraries.
Genome_build: mm10
|
| |
|
| Submission date |
Oct 20, 2020 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Remy Vu |
| E-mail(s) |
phuongnv@uci.edu
|
| Organization name |
University of California, Irvine
|
| Street address |
D288 Med Sci I Health Sciences Rd
|
| City |
Irvine |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE159704 |
Ovol1 regulates psoriasis-like skin inflammation and epidermal hyperplasia |
|
| Relations |
| BioSample |
SAMN16489363 |
| SRA |
SRX9318361 |
