|
| Status |
Public on Aug 27, 2022 |
| Title |
PF-Quie-2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse primary pulmonary fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
cell cycle state: Quiescence
cell type: mouse primary pulmonary fibroblast
molecule type: rRNA depleted RNA
|
| Treatment protocol |
Cellular senescence was firstly synchronized by 16 hours 9 mM RO3306, and then induced by 5 mM Nutlin 3a for 48 hours. After that, 100 nM BI-2536 was treated to exclude proliferative cells for total 12 days.
|
| Growth protocol |
Cultured in DMEM with 10% FBS and 1X antibiotics under 5%O2 hypoxia incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions. Removal of rRNA from total RNA (1 mg) was carried out using NEBNext rRNA Depletion Kit (New England Biolabs).
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). After the conversion of the linear dsDNA libraries to single-stranded circular DNA libraries (Universal Library Conversion Kit, MGI Tech, Guangdong, China), the pooled libraries were sequenced on a DNBSEQ-G400RS (MGI Tech) using paired-end mode (2×100 bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequencing data were aligned to mouse reference genome (mm10) using Rsubread (v2.4.3). Raw counts were obtained from read alignments through refGene for gene counts or RepeatMasker annotation for TEs, and then further transferred into CPM by edgeR (v3.32.1).
After filtering out low-expression genes with CPM lower than 0.1, differential expression was analyzed with the linear model using limma (v3.46.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw element counts for every repeat elements and every sample
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Aug 27, 2022 |
| Contact name |
Teh-Wei Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
IMSUT
|
| Street address |
4 Chome-6-1 Shirokanedai
|
| City |
Minato City, Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE198397 |
Bulk RNA-seq of Quiescent and Nutlin3a-Induced Senescent mouse pulmonary fibroblasts |
|
| Relations |
| BioSample |
SAMN26578084 |
| SRA |
SRX14436895 |
