|
| Status |
Public on Apr 12, 2024 |
| Title |
WT liver, 21 days keto, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
treatment: ketogenic diet, 21 days
|
| Treatment protocol |
At 4 weeks old, mice were fed either standard chow diet or ketogenic diet (90% fat, 9.7% protein, 0.3% carb) for 21 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by Triazol and Qiagen RNeasy Plus Mini kit. RNA quality was determined by BioAnalyzer and RIN > 4. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Liver tissue from WT C57BL/6 mice was collected after feeding with ketogenic diet for 21 days.
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using HISAT2 (v2.1.0) default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts (v1.5.0) to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName
|
| |
|
| Submission date |
May 31, 2023 |
| Last update date |
Apr 12, 2024 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE233831 |
Ketogenic diet induces p53-dependent cell senescence in multiple organs |
|
| Relations |
| BioSample |
SAMN35546704 |
| SRA |
SRX20554216 |
