|
| Status |
Public on Nov 25, 2024 |
| Title |
KO, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: Etnppl KO
treatment: 20 week Chow diet
Sex: female
|
| Treatment protocol |
Livers were harvested and snap frozen.
|
| Growth protocol |
Etnppl KO and WT mice were fed a chow diet for 20 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Trizol, cleaned up with RNEasy columns.mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA was synthesized from heat-denaturated purified mRNA using the following kits: a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) to synthesize first-strand cDNA; PCR Clean DX (Aline Biosciences) bead purification; and the NEBNext Ultra 12 Directional Second Strand cDNA Synthesis protocol (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KO3
|
| Data processing |
STAR[1](version 2.5.2b) was used to align RNA-Seq data to the genome reference; RSEM[2](version 1.3.0) was used to quantify gene and isoform expression; Ensembl gene annotation GTF[3]was used to build the RSEM reference, and add gene and transcript specific information to the .results file
Differential expression (DE) analysis was performed using R[4](version R-4.0.2) and DESeq2[5]package (version 1.28.1), using raw read count (gene-level abundances) as input data. When applying DESeq2, the functions DESeqDataSetFromMatrix and DESeq were used.
When performing DE analysis, genes were filtered out if the median counts from either test group or control group < 25. An expected Benjamini-Hochberg (FDR) adjusted p-value less than 0.05 as regarded as significant
Fold enrichment analysis was performed to determine biological processes that were up or down regulated.
GO terms were determined with the online DAVID resource with default parameters
Assembly: mm10
Supplementary files format and content: Tab delimited text files, with columns for NCBI official gene symbol, Ensembl gene ID, and FPKM values for each animal
|
| |
|
| Submission date |
Jul 08, 2024 |
| Last update date |
Nov 25, 2024 |
| Contact name |
René Jacobs |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Alberta
|
| Department |
Department of Agricultural, Food and Nutritional Science
|
| Lab |
Dr. Rene Jacobs laboratory
|
| Street address |
Room 4002E, Li Ka Shing Building, 11300 87 Ave NW
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2E1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE271787 |
The effect of ethanolamine phosphate phosphorylase knockout on hepatic gene expression |
|
| Relations |
| BioSample |
SAMN42381024 |
| SRA |
SRX25248026 |
