|
| Status |
Public on Nov 26, 2018 |
| Title |
Sample9: High-fat-female |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: SM/J
tissue: Liver
Sex: female
|
| Growth protocol |
Liver tissue was isolated from SM/J mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQ files were aligned to the Ensembl release 76 assembly using STAR version 2.0.4b
Gene count analysis in EdgeR; differences in library size accounted for with a TMM normalization, genes with counts of zero filtered out
Weighted likelihoods calculated using the voom function in the R package Limma, based on the mean-variance relationship of each gene and transcript
Generalized linear models were used to test for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene counts (RPKM values) for each sample
|
| |
|
| Submission date |
Oct 19, 2018 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Madeline Keleher |
| Organization name |
University of Colorado Anschutz
|
| Department |
Pediatrics
|
| Street address |
12700 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE121525 |
Effect of high-fat diet on hepatic gene expression in SM/J mice |
|
| Relations |
| BioSample |
SAMN10261073 |
| SRA |
SRX4907717 |
