|
| Status |
Public on May 07, 2021 |
| Title |
PBS_SD |
| Sample type |
SRA |
| |
|
| Source name |
PBS_SD_dorsal skin
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6
Sex: male
treatment: 48 hours post-mock-infection
diet: Standard diet
tissue: Dorsal skin
|
| Growth protocol |
N/A. Primary cells were used in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were isolated as previously described (Guerrero-Juarez, et al. Nat Commun. 2019)
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v3 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at the UCI Genomics High Throughput Facility at the University of California, Irvine.
Single Cell 3’ v3 chemistry - 10X Genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mRNA from single cells
|
| Data processing |
Transcripts from mice were mapped to the reference genome (GRCm38.93/mm10) using Cell Ranger Version 3.0.2
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Analysis of all data sets was performed using Seurat (Version 3.0.0)
Genome_build: mm10
Genome_build: GRCm38.39
Supplementary_files_format_and_content: Seurat output
|
| |
|
| Submission date |
May 17, 2020 |
| Last update date |
May 09, 2021 |
| Contact name |
Maksim V Plikus |
| E-mail(s) |
plikus@uci.edu
|
| Phone |
949-824-1260
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Street address |
845 Health Sciences Road
|
| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE150729 |
Diet-induced obesity promotes infection by impairment of the innate antimicrobial defense function of dermal adipocyte progenitors |
|
| Relations |
| BioSample |
SAMN14943471 |
| SRA |
SRX8356236 |
