|
| Status |
Public on Feb 27, 2024 |
| Title |
B13, HFD.ATM.exos, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
stromal vascular cells (SVCs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: stromal vascular cells (SVCs)
library id: JB_843
sample id: B13
condition: HFD.ATM.exos
|
| Treatment protocol |
8-week old weight-matched mice were fed 10 weeks a lard-based high-fat diet (HFD: 60% fat; Research Diets) and then treated for the last months of HFD-feeding with Rosigliatzone (3 mg/kg BW/day) or ATM-Exosomes (10^9 Exos/ i.v. injection twice per week).
|
| Growth protocol |
Male mice were ordered from Jackson Lab (C57BL/6, Stock 000664)and kept in the animal facility at the University of California, San Diego under SPF conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Epididymal fat was isolated, enzymatically digested in a collagen solution, and after red blood cells were lyzed and a cell vaibility of 80-90% confirmed, stromal vascular cells were used for scRNA-seqencing.
Cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
bcl2fastq was used to demultiplex shallow sequenced BCL files into FASTQ files
cellranger count was used to perform alignment, filtering, barcode counting and UMI counting for both shallow sequenced and deep sequenced FASTQ files
Assembly: mm10
Supplementary files format and content: Matrix files
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Feb 27, 2024 |
| Contact name |
Theresa Rohm |
| E-mail(s) |
trohm@health.ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE234046 |
Single-cell RNA-sequencing of stromal vascular cells (SVCs) from the epididymal fat of obese mice. |
|
| Relations |
| BioSample |
SAMN35573931 |
| SRA |
SRX20585713 |
