 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 01, 2023 |
| Title |
HFD; scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Epididymal white adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Epididymal white adipose tissue
Sex: male
cell type: stromal vascular fraction
age: 18 weeks old
strain: C57BL/6J wild type
treatment: high fat diet (HFD)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were washed by PBS to remove the remaining blood cells and then cut into small pieces.These small pieces were digested with Type II collagenase at 1 mg ml-1 for 30 min at 37 ℃ while shaking at 120 rpm. The samples were prepared into single-cell suspensions, Cell counts and cell viability were measured with the Countess® II Automated Cell Counter with cell activity above 80%, and cell concentrations were adjusted to the ideal concentration of 1000 /μL.
scRNA-seq libraries were generated using the Chromium Single Cell 3' Library and Gel Bead Kit V3 (10X Genomics, 1000075), Chromium Single Cell B Chip kit (10X Genomics, 1000074), and Chromium i7 Multiplex Kit (10X Genomics, 120262). Cells were resuspended in reverse transcription enzyme mix and loaded onto the Chromium Single Cell B Chip to generate gel beads-in-emulsion of 6,000 cells per channel. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio-Rad). The cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. ScRNA-seq libraries were constructed using Single Cell 3' Library and Gel Bead Kit V3 and finally sequenced using an Illumina NovaSeq 6000 instrument with a sequencing depth of at least 50,000 reads per cell with paired-end 150-bp reading strategy.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
The Cell Ranger software was obtained from 10× Genomics website. Alignment, filtering, barcode counting, and UMI counting were performed with cell ranger count module on the raw sequencing data to generate a gene-barcode matrix for subsequent analysis.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software with the Seurat package.
Before the downstream analysis, low-quality cells were excluded and retained the high-quality single-cell data that met the following criterial: Briefly, cells with a detected gene count less than 300 or exceeding 4000, or mitochondrial gene ratio was more than 10%, or an nCount exceeding 15000 were filtered out. Additionally, genes expressed in fewer than 5 cells were removed.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jul 12, 2023 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Limin Xie |
| E-mail(s) |
xielimindr@gmail.com
|
| Phone |
13927573262
|
| Organization name |
The second xiangya hospital of central south university
|
| Street address |
No.139，Renmin Road Central Changsha, Hunan, China
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410011 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE237143 |
Single-cell transcriptome of stromal vascular fraction isolated from adipose tissue of lean and obese mice |
|
| Relations |
| BioSample |
SAMN36417032 |
| SRA |
SRX20995417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7596044_HFD_barcodes.tsv.gz |
27.0 Kb |
(ftp)(http) |
TSV |
| GSM7596044_HFD_genes.tsv.gz |
212.7 Kb |
(ftp)(http) |
TSV |
| GSM7596044_HFD_matrix.mtx.gz |
23.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
