|
| Status |
Public on Jun 14, 2022 |
| Title |
High fat - high sugar diet_rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6NJ
Sex: Male
tissue: Liver
diet: High fat + high sugar diet
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Livers were flash frozen in liquid nitrogen, homogenized in Trizol (Invitrogen), and total RNA was isolated with the RNeasy mini kit (Qiagen). 1 µg of total RNA was used to isolate polyA RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) and polyA RNA was enriched with the SMARTer Apollo NGS library prep system (Takara Bio USA, Mountain View, CA).
The library was prepared with the dUTP-based stranded library NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were preprocessed using Illumina BaseSpace.
Reads were aligned using STAR (Aligner) version 2.6.1a. Gene counts were quantified for each sample based on the number of aligned reads that match each annotated gene using RnaReadCounter tool within the BaseSpace RNA-Seq Alignment app v2.0.2 to generate Counts Per Million (CPM).
Genome_build: mm10
|
| |
|
| Submission date |
Mar 03, 2022 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Mikhail Dozmorov |
| E-mail(s) |
[email protected]
|
| Organization name |
Virginia Commonwealth University
|
| Department |
Biostatistics
|
| Street address |
830 E Main St
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE197884 |
A NEW PRECLINICAL MODEL OF WESTERN DIET-INDUCED PROGRESSION OF NON-ALCOHOLIC STEATOHEPATITIS TO HEPATOCELLULAR CARCINOMA |
|
| Relations |
| BioSample |
SAMN26420135 |
| SRA |
SRX14361459 |
