|
| Status |
Public on Apr 27, 2023 |
| Title |
NF-4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
group: SPF
8w or 24w: 8W
diet: LF
|
| Treatment protocol |
Mice were fed one of four purified diets for 8 or 24 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed and a small section was placed directly in Trizol for subsequent RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw fastq files generated from the RNA-seq analysis were examined by the fastqc to evaluate the quality
The STAR aligner (version 2.4.2a) was used to map the raw reads to the reference mouse genome
The genetic features from Gencode (version M23) were extracted from the resulting bam file produced by STAR
The raw gene expression count matrix was then generated by featureCounts (version subread-1.4.6-p1)
EdgeR (version 3.22.5) was used to filter low-expressed genes where genes expressed below ten counts-per-million (CPM) in 4 samples were removed
Limma-Voom pipeline (version 3.38.3) was applied to normalize the filtered count matrix and perform differential gene expression analysis for pairwise comparisons
Enrichment analysis on significant DEGs with mouse-specific GO terms and KEGG pathways was conducted through Lynx
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene
|
| |
|
| Submission date |
Dec 15, 2021 |
| Last update date |
Apr 27, 2023 |
| Contact name |
Vanessa Leone |
| E-mail(s) |
valeone@wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Street address |
1933 Observatory Dr.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE190982 |
Imbalanced gut microbiota drives nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model |
|
| Relations |
| BioSample |
SAMN24103018 |
| SRA |
SRX13439722 |
