|
| Status |
Public on Jan 30, 2020 |
| Title |
71-HFD control |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
sample id: 15089X11
diet: High fat diet
treatment: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30-50 mg tissue was homogenized using bullet blender and the lysate was used for the RNA extraction using the RNAeasy kit (Qiagen) as per the manufacturer instructions
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jan 30, 2020 |
| Contact name |
Chris Stubben |
| Organization name |
Huntsman Cancer Institute
|
| Department |
University of Utah
|
| Street address |
2000 Cir of Hope Dr
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84103 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE132056 |
Removing a Double Bond from Ceramides Ameliorates Insulin Resistance and Hepatic Steatosis |
|
| Relations |
| BioSample |
SAMN11918192 |
| SRA |
SRX5944720 |
