|
| Status |
Public on Sep 01, 2020 |
| Title |
Control sample 6 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6J (B6)
diet: control
|
| Treatment protocol |
At experiment initiation, mice (n = 11/group) were randomized to control diet or a matched diet containing BIBB-515 (dosed at 55 mg/kg body weight).
|
| Growth protocol |
Six-week-old female C57BL/6J (B6) mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and acclimated for two weeks prior to initiation of experiments. Mice were housed three or four per cage and maintained at 22ºC under a 12-hour light cycle. Mice were maintained in accordance with University of California, Los Angeles Institution Animal Care and Use Committee protocols. Three days prior to initiation of experiments, all mice were switched from a chow diet (Ralston Purina Company) to the control diet (Research Diets D111112201) (kcal= 15% fat, 65% carbohydrate, 20% protein).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flash frozen hepatic samples were homogenized in Qiazol (QIAGEN) and RNA isolated according to the manufacturer’s protocol with RNeasy columns (QIAGEN). Isolated RNA was converted to cDNA using a High Capacity cDNA Synthesis Kit (ThermoFisher) according to the manufacturer’s instructions.
Primers targeted at genes of interest were designed and reactions were run in triplicate using KAPA SYBR FAST qPCR Master Mix (Roche) with 8 ng of cDNA per reaction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
control_6
|
| Data processing |
Quality control metrics were calculated using RNA-SeQC v1.1.7
Sequenced reads were aligned using STAR v2.5.3a
Reads were quantified using the featureCounts tool from the Subread package v1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files output from featureCounts using various options. Options used to generate each file are shown in the first line of the file.
|
| |
|
| Submission date |
Aug 31, 2020 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Daniel Michael Jordan |
| E-mail(s) |
daniel.jordan1@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1 Gustave L Levy Place, box 1498
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE157223 |
An integrative multiomic network model links the canonical lipid metabolism pathway to glucose regulation in coronary artery disease |
|
| Relations |
| BioSample |
SAMN15950505 |
| SRA |
SRX9047148 |
