|
| Status |
Public on Mar 31, 2018 |
| Title |
WAF-control-1 (A518_2) |
| Sample type |
SRA |
| |
|
| Source name |
white abdominal fat (WAF)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: white abdominal fat
age: 14 weeks
strain: C57BL/6-Lepob
treatment: DMSO
|
| Treatment protocol |
At 10 weeks of age mice were being injected, by IP injection, with vehicle only (DMSO diluted in PBS) or MS417. For the first 15 days mice were injected with a lower dose of 2.5mg/kg. For the remaining 2 weeks the higher 5mg/kg dose of MS417 was used.
|
| Growth protocol |
Male ob/ob B6 mice were obtained from Taconic. They were single caged and pair fed a regular chow diet where the amount of food given to each control mouse corresponded to the mean amount ate by treated mice, fed ad libitum, the previous day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
White abdominal fat (WAF) was removed, flash frozen, and RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared from Tryzol extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
A518_2
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
After filtering contaminant (aligned) reads, sequenced reads were then mapped to mm9 genome, RefSeq exons, splicing junctions using BWA v0.7.3 alignment algorithm
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Huber et al., Journal of immunology, 2012. In short, uniquely aligned reads to the exon and splicing-junction sites for each transcript were counted and normalized by the size of the transcript and by the size of the library.
RNA for RNA-seq was extracted from white abdominal fat collected from 2 control and 3 treated animals. Expression was compared between control and treated mice matched by weight at the beginning of the treatment ( A518_2/A518_1, A518_2/A518_3 and A518_5/A518_4). Expression change expressed as log2ratio for the 3 comparisons was then averaged.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin J. Walsh |
| E-mail(s) |
martin.walsh@mssm.edu
|
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Structural and Chemical Biology
|
| Street address |
One Gustave L. Levy Pl.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE59161 |
BRD4 links carbohydrate and lipid synthetic pathways to a core transcriptional network for a cell-type specific metabolic response (RNA-seq Fat) |
| GSE59162 |
BRD4 directs glycolytic metabolism through a comprehensive epigenomic and transcriptional network |
|
| Relations |
| BioSample |
SAMN02904566 |
| SRA |
SRX647410 |
