|
| Status |
Public on Nov 27, 2023 |
| Title |
e2-1: eWAT_Cont_siNS_2 |
| Sample type |
SRA |
| |
|
| Source name |
SVF-derived adipocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell type: SVF-derived adipocyte
tissue: epididymal white adipose tissue
strain: Senp2flox/flox
treatment: siNS
|
| Treatment protocol |
SVF from control and Senp2-aKO mice was treated with C/EBPβ-specific siRNA.
|
| Growth protocol |
Stromal vascular fraction (SVF) cells were isolated from the iWAT or eWAT. SVF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco Life Technologies) supplemented with 10 % FBS, and seeded in 12-well plates. Adipocyte differentiation of confluent SVF cells was induced by treatment with DMI (1 mol/l dexamethasone, 0.5 mmol/l isobutylmethyxanthine and 0.1 mg/ml insulin) in DMEM supplemented with 10 % FBS. Two days after the treatment, cells were maintained in DMEM supplemented with 10 % FBS and 1 μg/ml insulin for additional 5 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were isolated using TRIzol (Invitrogen, MA, USA) according to the manufacturer’s instruction.
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Seq Kit (NEW ENGLAND BioLabs, Inc., UK).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Sehyun Chae |
| E-mail(s) |
shchae@kbri.re.kr
|
| Organization name |
Korea Brain Research Institute
|
| Department |
Neurovascular Unit Research Group
|
| Street address |
61, Cheomdan-ro, Dong-gu
|
| City |
Daegu |
| ZIP/Postal code |
41062 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE189387 |
SENP2 suppresses browning of white adipose tissues by de-conjugating SUMO from C/EBPβ |
|
| Relations |
| BioSample |
SAMN23405372 |
| SRA |
SRX13205621 |
