|
| Status |
Public on Apr 30, 2023 |
| Title |
MRX372 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
Sex: male
strain: C57Bl/6J
diet: RF
dietary fat content: SAAR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from crushed and frozen livers using Direct-zol RNA Miniprep kit (R2052, Zymo Research) according to the manufacturer's instructions.
NEBNext Ultra II RNA Library Prep kit, performed by Genewiz (Azenta Life Sciences)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FastQC for quality control (pre trim)
Cutadapt for adapter and quality trimming
FastQC fo quality control (post trim)
kallisto for pseudoalignment
tximport for import into R (4.0.3)
DEseq2
Assembly: Mouse Ensembl Transcriptome v94
Supplementary files format and content: Post pseudoalignment; each individual sample file (.tsv) contains both est_counts and tpms
|
| |
|
| Submission date |
Apr 04, 2022 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Tracy G Anthony |
| E-mail(s) |
tracy.anthony@rutgers.edu
|
| Phone |
848-932-6331
|
| Organization name |
Rutgers University
|
| Department |
Nutritional Sciences
|
| Street address |
59 Dudley Rd
|
| City |
New Brunswick |
| State/province |
NJ |
| ZIP/Postal code |
08901 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE200149 |
Impact of dietary fat content and sulfur amino acid restriction on the hepatic transcriptome in male mice |
|
| Relations |
| BioSample |
SAMN27292865 |
| SRA |
SRX14733022 |
