|
| Status |
Public on Apr 01, 2024 |
| Title |
primary murine hepatocytes, GW+C29, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: primary murie hepatocytes
treatment: GW+C29
|
| Treatment protocol |
After overnight starvation, the mice were intraperitoneally injected with solvent control, GW7647 (4mg/kg) and/or Compound 29 (10mg/kg) dissolved in Ringer solution. The mice were sacrificed 4h after injection. Liver tissue was isolated, snap frozen and stored at -80°C.
|
| Growth protocol |
Mice were maintained in a pathogen-free animal facility under standard 12h light/12 dark cycle, with access to chow and water ad libitum. For the hepatic RNA expression studies, C57Bl/6J (wild-type) male mice, 11 weeks of age, were randomly divided in 4 groups of 6 mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the murine livers was isolated using TRIzol Reagent, according to the manufacturer’s protocol (Invitrogen).
RNA sequencing libraries were generated in biological triplicate (3 mice were used per condition) using the TruSeq stranded mRNA protocol. Libraries were subjected to single-end 100bp sequencing on Illumina NovaSeq6000, yielding 12-20 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data analysis was performed using a dedicated Snakemake pipeline. Trim-Galore (version 0.6.6-0) was used to trim low-quality ends from reads (with phred score < 30), in addition to adapter removal.
Trimmed reads were pre-mapped to PhiX genome using STAR (version 2.7.6a) with a genome index setting --genomeSAindexNbases 5, disabled splicing and a maximum of 2 mismatches allowed. The PhiX-unmapped reads were then aligned to the mouse genome GRCm38 using the splice junctions of the Ensembl 101 annotation, allowing only uniquely mapped reads and a maximum of 4 mismatches.
The position-sorted output BAM files were converted to count data using HTSeq (version 0.12.4) in the ‘union’ mode.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Apr 12, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Karolien De Bosscher |
| E-mail(s) |
karolien.debosscher@vib-ugent.be
|
| Organization name |
VIB-UGent Center for Medical Biotechnology
|
| Street address |
Technologiepark-Zwijnaarde 75
|
| City |
Gent |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE200658 |
The nuclear receptors ERRα and PPARα co-ordinately control starvation-induced gene expression in hepatocytes. |
|
| Relations |
| BioSample |
SAMN27534024 |
| SRA |
SRX14830545 |
