 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2024 |
| Title |
WT_CHOW_1 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: WT
treatment: chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the livers of the mice after tissue disruption with the TissueRuptor (Qiagen) with the RNeasy kit (Qiagen, 75162), according to the manufacturer’s protocol
The non-directoinaly librabry protocol of Novogene was performed on site. Briefly, Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The cDNA was ready for sequencing after end repair, A-tailing, adapter ligation, size selection, amplification, and purification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
C1CHW
|
| Data processing |
The quality of the raw sequencing reads was evaluated using FastQC (v0.11.5)
Alignment to genome reference consortium mouse build 38 (GRCm38) was performed with the STAR (v.2.7.3a) tool
Differential gene expression and pathway analysis were performed using DESeq2 R package software41 and the Omics Playground tool (v2.8.12) platform
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Jul 25, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Claudia Theys |
| E-mail(s) |
claudia.theys@uantwerpen.be
|
| Organization name |
Universiteit Antwerpen
|
| Department |
FBD
|
| Lab |
PPES
|
| Street address |
Universiteitsplein,1
|
| City |
Wilrijk |
| State/province |
Antwerpen (nl) |
| ZIP/Postal code |
2610 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE238201 |
Loss of PPARα function promotes epigenetic dysregulation of lipid homeostasis driving ferroptosis and pyroptosis lipotoxicity in Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) [RNA-seq] |
| GSE239279 |
Loss of PPARα function promotes epigenetic dysregulation of lipid homeostasis driving ferroptosis and pyroptosis lipotoxicity in Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) |
|
| Relations |
| BioSample |
SAMN36703992 |
| SRA |
SRX21154658 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
