|
| Status |
Public on Aug 18, 2023 |
| Title |
Liver high-fat diet ERRa KO biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: ERRa KO (Esrra KO)
strain: C57BL/6N
Sex: male
treatment: 15-week high-fat diet
|
| Treatment protocol |
WT and ERRa KO mice on a C57BL/6N genetic background fed either a chow or high-fat diet (HFD) for 15 weeks initiated from 6 weeks of age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen liver using a RNeasy Mini Kit (QIAGEN).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of FASTQ format were processed through fastp to remove reads containing adapter and poly-N sequences and reads with low quality.
Paired-end clean reads were aligned to the Mus musculus reference genome GRCm38/mm10 using the Spliced Transcripts Alignment to a Reference (STAR) software version 2.5 (mismatch = 2).
HTSeq version 0.6.1 (-m union) was used to count the read numbers mapped of each gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including the read count values for all 16 samples
Supplementary files format and content: tab-delimited text file including the fpkm values for all 16 samples
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Aug 18, 2023 |
| Contact name |
Vincent Giguère |
| E-mail(s) |
vincent.giguere@mcgill.ca
|
| Phone |
514-398-5899
|
| Organization name |
McGill University
|
| Department |
Goodman Cancer Centre
|
| Street address |
1160 Pine Ave West, McIntyre Bldg Room 710
|
| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H3A 1A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE205846 |
Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression [RNA-Seq] |
| GSE205847 |
Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression |
|
| Relations |
| BioSample |
SAMN28964628 |
| SRA |
SRX15672435 |
