|
| Status |
Public on Nov 01, 2018 |
| Title |
Ctrl-3-scWAT |
| Sample type |
SRA |
| |
|
| Source name |
scWAT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: scWAT
group: Ctrl
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from fat tissue were extract by RNeasy Mini Kit (Qiagen) according to manufacturer’s recommendations and validated by the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA).
150 bp paired-end reads were sequenced on Illumina Hiseq Xten platform in CapitalBio technology corporation (Beijng).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The paired-end clean reads were aligned to the reference genome using STAR and each gene reads numbers were count by HTseq.
Differential expression gene (DEG) analysis was performed by DEseq2 package in which gene length and dispersion bias was corrected.
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: SUB_readcount.csv: raw_counts_scWAT
Supplementary_files_format_and_content: EP_readcount.csv: raw_counts_pgVAT
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
Nov 01, 2018 |
| Contact name |
Li Li |
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE117843 |
Microbiota Depletion Impairs Adaptive Thermogenesis of Both Brown and Beige Adipose Tissue |
|
| Relations |
| BioSample |
SAMN09737979 |
| SRA |
SRX4483214 |
