|
| Status |
Public on Feb 23, 2023 |
| Title |
Cohort_4, omental, subject_2 |
| Sample type |
SRA |
| |
|
| Source name |
Omental white adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Omental white adipose tissue
cohort: Cohort_4, subject_2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Paired samples of omental and subcutaneous WAT were obtained from female patients with obesity undergoing different bariatric surgery procedures (Roux-en-Y Gastric Bypass and sleeve gastrectomy). After collection, samples were washed using PBS, placed on ice until the end of the surgery procedure, snap-frozen in liquid nitrogen and stored at -80°C for later use.
50 mg of fresh or frozen WAT was first minced into 1-3 mm pieces and then homogenized on ice in 0.1% CHAPS in CST buffer supplemented with 0.2U/μl RNAase inhibitor (RI) using a Dounce homogenizer. After homogenization, samples were left on ice for five minutes following which PBS supplemented with BSA and 0.2U/μl RI was added to obtain a final concentration of 1% BSA. The lysates were filtered through 40 μm cell strainers and centrifuged at 500 x g for five minutes at 4 °C. The nuclei pellets were resuspended with 1% BSA in PBS supplemented with 0.2U/μl RI and centrifuged again at 500 x g for five minutes at 4 °C. This step was repeated once more. After the final resuspension, nuclei were filtered through 20 μm cell strainers and loaded directly on a 10x Chip G. 10X-libraries were prepared with the Chromium Single Cell v3.1 reagent kit following the manufacturer’s protocol (10X Genomics). Suspensions containing around 1200 nuclei per μl were loaded on Chip G followed by reverse transcription to obtain cDNA, which subsequently was amplified and used for library construction. After preparation, the libraries were sequenced on a NovaSeq 6000 platform (Illumina).
snRNA-seq
|
| |
|
| 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 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Feb 21, 2023 |
| Last update date |
Feb 23, 2023 |
| Contact name |
Jiawei Zhong |
| Organization name |
Karolinska Institutet
|
| Department |
Department of Medicine, Huddinge
|
| Lab |
Mikael Rydén & Niklas Mejhert lab
|
| Street address |
Blickagången 16, Flemingsberg
|
| City |
Stockholm |
| ZIP/Postal code |
14182 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE225700 |
snRNA-seq data on human subcutaneous and omental white adipose tissue |
|
| Relations |
| BioSample |
SAMN33392646 |
| SRA |
SRX19452686 |
