|
| Status |
Public on May 09, 2018 |
| Title |
WT HFHCD 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
acox1 genotype: Wildtype
background: C57BL/6
diet: Chow for 8 weeks, followed by high-fat, high-carb for 4 weeks
age at sacrifice: 12 weeks
Sex: Male
|
| Treatment protocol |
Wildtype and Acox1Lampe1 mice were fed either regular chow (fat 13.5%kcal, carbohydrate 59%kcal, protein 27.5 kcal) for 12 weeks, or regular chow for 8 weeks followed by 4 weeks on high-fat high-carbohydrate (fat 58% kcal, carbohydrate 25.5% kcal, protein 16.4 kcal).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ilumina TruSeq. RNA was isolated using Trizol and cleaned using Quiagen Cleanup kit
Standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Liver from Wildtype Male Mus musculus fed Chow for 8 weeks, followed by high-fat, high-carb for 4 weeks
|
| Data processing |
Illumina HiSeq2000 was used for base calling
Following adapter and barcode trimming, high-quality raw reads were aligned (mm8 mouse genome using Ensembl annotations) and quantified using the TopHap Cufflinks pipeline.
Computed RPKM were normalized using a 75th percentil shift and baselined to the median of all samples.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited with gene symbol and RPKM.
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
May 09, 2018 |
| Contact name |
Rebekah Karns |
| E-mail(s) |
[email protected]
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Gastroenterology, Hepatology, & Nutrition
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45276 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE89626 |
Identifying the role of Acox1 in metabolism and inflammation in non-alcoholic fatty liver disease through mRNA-sequencing. |
|
| Relations |
| BioSample |
SAMN05991619 |
