|
| Status |
Public on May 14, 2019 |
| Title |
HFD-IAT_Stromal vascular cells 1 |
| Sample type |
SRA |
| |
|
| Source name |
Stromal vascular cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Stromal vascular cells
cell type: SVC
|
| Treatment protocol |
None
|
| Growth protocol |
8 week old C57BL/6J male mice were fed HFD for 10 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
EAT and IAT were isolated from HFD-fed mice. Each adipose tissues were incubated with collagenase I buffer to separate adipocyte and SVCs.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina 1.9 was used for base calling.
Read pairs were aligned using RSEM v.1.2.25 and Bowtie 2.2.6 to the Mus musculus genome (GRCm38/mm10).
Expected number of fragments from each transcript and gene were estimated with RSEM.
Limma (Voom) v.3.14.4 was used to perform statistical tests for pairwise differential expression between samples, calculate log2 fold change (log2FC) values and select DEGs with adjusted p-value cutoff <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expected counts, TPM, RPKM values for each sample.
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
May 15, 2019 |
| Contact name |
Jae Bum Kim |
| E-mail(s) |
jaebkim@snu.ac.kr
|
| Phone |
+82-2-880-4409
|
| Organization name |
Seoul National University
|
| Department |
School of Biological Sciences
|
| Lab |
Lab. of Adipocyte and Metabolism Research
|
| Street address |
Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu
|
| City |
Seoul |
| ZIP/Postal code |
156-742 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE129665 |
RNA-sequencing of adipocyte and stromal vascular cells (SVCs) of epididymal and inguinal adipose tissue from high-fat diet (HFD)-fed mice |
|
| Relations |
| BioSample |
SAMN11399035 |
| SRA |
SRX5669870 |
