|
| Status |
Public on Jul 08, 2020 |
| Title |
KO brown fat 2 |
| Sample type |
SRA |
| |
|
| Source name |
KO brown fat
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
age: 6 weeks old
genotype/variation: PHOSPHO1 knockout (KO)
tissue: mature brown fat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mature brown fat is isolated from minced adipose tissues which were digested with collagenase A. The mature adipocytes was obtaibed in the upper lipids layer after centrifugation at 700 g for 5 min. RNA were extracted using QIazol reagent and RNAeasy kit (Qiagen.)
mRNA library was prepared using KAPA Hyper mRNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
single-end sequencing (50 cycles). Sequences were aligned to mouse genome (mm9) using STAR (version 2.5.4b) with Ensembl gene model version 67. After reads were checked for strandness with infer_experiment.py function from RSeQC , only reverse stranded reads were assigned to genes with STAR.
Genome_build: mm9
Supplementary_files_format_and_content: gene counts in text
|
| |
|
| Submission date |
Mar 29, 2019 |
| Last update date |
Jul 08, 2020 |
| Contact name |
Nai-Jia Huang |
| E-mail(s) |
njhuang@wi.mit.edu
|
| Organization name |
Whitehead Institute
|
| Lab |
Harvey Lodish
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE129020 |
RNA sequencing of wildtype and PHOSPHO1 knockout brown fat |
|
| Relations |
| BioSample |
SAMN11284178 |
| SRA |
SRX5598390 |
