|
| Status |
Public on Feb 22, 2023 |
| Title |
A_15_2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
Sex: Male
cell type: Bulk liver
genotype: Wild-type
treatment: Control diet
timepoint: 15m
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using NEBNext Ultra II non-directional RNA Library Prep kit (New England Biolabs, Inc., Ipswich, MA, USA). Library quality and concentration were assessed with Labchip and qPCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The NovaSeq 6000 uses RTA3 for its base calling. The version running on our machines is v3.4.4.
RNA-Seq data was analyzed using a Salmon-tximport-DESeq2 pipeline. The pair-ended reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm39, GENCODE release 27) and quantified with Salmon.
Gene-level counts were imported with tximport and differential expression analysis was performed with DESeq2 (version 1.18) with the corrected p value < 0.05 and fold change > 2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized read count values for each sample
|
| |
|
| Submission date |
Oct 23, 2022 |
| Last update date |
Feb 22, 2023 |
| Contact name |
Guiyan Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California at Davis
|
| Department |
Department of Medical Pathology and Laboratory Medicine
|
| Lab |
Wan Lab
|
| Street address |
4645 2nd Ave
|
| City |
Sacramento |
| State/province |
CA |
| ZIP/Postal code |
95817 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216375 |
The essential roles of FXR in diet and aging affected metabolic changes and liver disease development: a multi-omics study |
|
| Relations |
| BioSample |
SAMN31420425 |
| SRA |
SRX17998761 |
