|
| Status |
Public on Oct 02, 2023 |
| Title |
Bulk RNAseq Cyr61 KO rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cyr61fl/fl
gender: Male
age: 24 weeks
genotype: Cyr61KO
|
| Treatment protocol |
12 weeks NASH diet (Tsuchida et al., 2018)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
livers were removed and flash frozen in liquid nitrogen. RNA was extracted with Nebnext II directional library prep kit and 1ug was used per library.
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 |
| |
|
| Description |
Bulk RNAseq Cyr61 KO rep3
|
| Data processing |
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to human reference hg38 by STAR aligner (version 2.6.1a)
Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.6.1a)
Assembly: mm10
Supplementary files format and content: Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.6.1a)
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
203 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE199637 |
CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages [bulk RNA-seq] |
| GSE199640 |
CYR61 orchestrates NASH fibrosis through SYK-NFκB-PDGF signaling in monocyte-derived macrophages |
|
| Relations |
| BioSample |
SAMN27028647 |
| SRA |
SRX14642914 |
