|
| Status |
Public on Mar 01, 2018 |
| Title |
Warm white adipocyte mRNA rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
inguinal WAT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: adipose
|
| Treatment protocol |
Mice were exposed to cold (4°C for 1 week (cold brown/beige adipocyte samples), and subsequently incubated at 30°C for 4 weeks (warm brown/beige adipocyte samples). Mice born and maintained at 30°C at all times used for warm white adipocyte samples.
|
| Growth protocol |
Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRAP was performed as previously described (Roh et al., Cell Rep 2017). Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
TRAP-isolated RNA (≤100ng) was treated with the Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module. cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit. Sequencing libraries were analyzed Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM, and sequenced on a HiSeq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biological replicate
mRNA_NuTRAP_iWAT_white_rewarm_003_001_001
|
| Data processing |
RNA-seq data were aligned to the mm10 mouse genome using HISAT2 (Kim et al., 2015).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM≥2) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥1 and log2 false discovery rate (FDR)≤0.05
Gene set enrichment analysis was performed using DAVID Bioinformatics Resources 6.8 (Huang da et al., 2009) and summarized by REVIGO (Supek et al., 2011).
Genome_build: mm10
Supplementary_files_format_and_content: read counts with batch normalization
|
| |
|
| Submission date |
Dec 14, 2017 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Evan Rosen |
| E-mail(s) |
erosen@bidmc.harvard.edu
|
| Organization name |
Beth Israel Deconess Medical Center
|
| Department |
Endocrinology
|
| Lab |
Rosen Lab
|
| Street address |
3 Blackfan Cir
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE108077 |
Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity |
|
| Relations |
| BioSample |
SAMN08177625 |
| SRA |
SRX3471213 |
