|
| Status |
Public on Feb 05, 2024 |
| Title |
myofibroblast, KO, treated, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary renal myofibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary renal myofibroblasts
genotype: KO
treatment: TGFb1-treated
strain: C57BL/6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary renal myofibroblasts were harvested and RNA was extracted with RNeasy mini kit (Qiagen) following the manufacturer’s instruction.
Libraries were generated with the poly-A selection method (mRNA Direct kit, Life Technologies) and sequenced with the NovaSeq 6000 S4 platform (23150 bp) at a target of 30 million reads per library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HO_T_1
|
| Data processing |
Libraries were sequenced by illumine sequencer Novaseq of 150 bp pair-end reads.
Reads were mapped to mouse genome GRCm38 (mm10) v89 using STAR6 aligner and counts per gene were quantified by featureCounts7 with settings of pair-end (-p) and exon mapping (-t exon).
Preprocessing filtering removed genes not expressed in more than one sample.
Genes were considered detected if they have a count of at least 5 counts in at least 5 samples.
Assembly: mm10
Supplementary files format and content: tab seperated raw count file (combined all samples)
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Jing Guo |
| E-mail(s) |
jing.guo@duke-nus.edu.sg
|
| Organization name |
Duke-NUS Medical School
|
| Department |
Center for Computational Biology
|
| Street address |
8 Collage Road, DUKE-NUS Medical School, level 5
|
| City |
Singapore |
| State/province |
State... |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE241503 |
WWP2 MEDIATES THE METABOLIC REPROGRAMMING OF RENAL MYOFIBROBLASTS TO PROMOTE KIDNEY FIBROSIS [bulk RNA-seq] |
| GSE241504 |
WWP2 MEDIATES THE METABOLIC REPROGRAMMING OF RENAL MYOFIBROBLASTS TO PROMOTE KIDNEY FIBROSIS |
|
| Relations |
| BioSample |
SAMN37120549 |
| SRA |
SRX21463074 |
