|
| Status |
Public on Feb 19, 2024 |
| Title |
MEFs,PtenĪ±-/-,VSV 8h,rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblast cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast cells
genotype: Pten{alpha} KO
infection: VSV
|
| Treatment protocol |
Cells were treated with VSV for eight hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Zeliang Yang |
| E-mail(s) |
zeliangy@bjmu.edu.cn
|
| Organization name |
Peking University Health Science Center
|
| Street address |
No.38 Xueyuan Road,Haidian
|
| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE210684 |
RNA-seq of wild-type and PtenĪ±-/- MEFs under VSV infection |
|
| Relations |
| BioSample |
SAMN30185055 |
| SRA |
SRX16974292 |
