|
| Status |
Public on Dec 31, 2022 |
| Title |
liver, D4 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: ob/ob
tissue: liver
diet: GAN
phenotype: NASH
treatment: DGAT2-GalNac 1473 siRNA
|
| Treatment protocol |
Ten-week-old genetically obese ob/ob mice (n=4) were injected subcutaneously with either non targeting control NTC (10mg/kg) or Dgat2-1473 (10mg/kg) and provided a NASH-inducing diet (GAN diet) for 3 weeks. After 3 weeks mice were sacrificed.
|
| Growth protocol |
10w old ob/ob mice fed with NASH diet for 3 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
DolphinNext RNASeq Pipeline Trimmomatic (v.0.11.8) step removed Illumina adapter sequences
DolphinNext RNASeq Pipeline RSEM (v.1.2.28) aligned reads with the STAR aligner and then estimated expression levels, producing rsem_gene_expected_count.tsv
DEBrowser's DESeq2 module was used to find differentially expressed genes using the RSEM levels
The enrichGO function of the clusterProfiler package found pathways associated with the differentially expressed genes
rsem -star was used to produce rsem_gene_expected_count.tsv which is a tab delimited text file. Note: this data is NOT normalized.
Genome_build: mm10
Supplementary_files_format_and_content: rsem_gene_expected_count.tsv
|
| |
|
| Submission date |
Jun 27, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Michael Czech |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Street address |
373 Plantation Street
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE178987 |
An RNAi therapeutic targeting hepatic DGAT2 in a genetically obese mouse model of nonalcoholic steatohepatitis |
|
| Relations |
| BioSample |
SAMN19904626 |
| SRA |
SRX11237950 |
