|
| Status |
Public on Apr 12, 2024 |
| Title |
liver, WT, fasted, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
Sex: male
strain: C57Bl/6J
genotype: WT
treatment: fasted
|
| Treatment protocol |
Mice in the fasted group were food denied for 48 hours, but all mice were given free access to water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy Kit
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using STAR-RSEM default settings to obtain the counts per gene
Gene count measurements were obtained directly from RSEM algorithm
Assembly: mm10
Supplementary files format and content: The processed data files are in tabular format, which contains gene_id, transcript_id(s), gene length, effective_length, expected_count, TPM, and FPKM
|
| |
|
| Submission date |
Feb 29, 2024 |
| 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) |
| GSE260582 |
Mitochondrial ACSS1-K-635 acetylation mimic knock-in mice exhibit altered lipid metabolism, hepatic cell senescence, and acute non-alcoholic fatty liver [2ndSet_analysis] |
|
| Relations |
| BioSample |
SAMN40202800 |
| SRA |
SRX23795161 |
