|
| Status |
Public on Sep 28, 2023 |
| Title |
Chow Diet + Vehicle, F55 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57/BL6
genotype: WT
treatment: Chow Diet + Vehicle
timepoint: 19 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen Bulk liver tissue was homogenized using Qiagen Tissue lyzer and tungsten carbide beads. RNA was harvested from homogenate by way of Trizol/ Chloroform extraction followed by RNeasy mini plus kit (Qiagen).
Libraries were made from 200ng of total RNA using the NEBNext UltraII RNA library preparation kit, following the manufacturer protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
ChowVEH55
S19
polyA
|
| Data processing |
Primary analysis RTA 3.9.25 and Secondary analysis DRAGEN GenerateFastQ 3.7.4.
Sequencing was conducted on an Illumina NextSeq 2000 system with 71 base pair single-end reads.
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a).
Gene based counting was performed using the STAR aligner (version 2.7.1a).
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.28.1).
Assembly: mm10
Supplementary files format and content: Rawcounts.csv: Comma-delimited text file includes raw counts for each Sample generated by STAR aligner.
|
| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Sep 28, 2023 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE224069 |
Effect of NMT inhibition on a model of NALFD in mice |
|
| Relations |
| BioSample |
SAMN32961521 |
| SRA |
SRX19216005 |
