|
| Status |
Public on Mar 12, 2019 |
| Title |
RIG-I-iCLIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: murine macrophage cell line
passages: 15-18
strain: C57BL/6
rip antibody: RIG-I (Cell Signaling technology,D14G6, 3743BC)
infection: RAW264.7 cells upon VSV infection for 8 hr
|
| Treatment protocol |
RAW264.7 cells were infected with VSV for 8 hr and then were crosslinked with UV at 254 nm for 300 mJ/cm2.
|
| Growth protocol |
RAW264.7 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iCLIP was performed usign anti-RIG-I antibody, and the isolated RNA was further processed into iCLIP-seq library and then standard illumina sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 4
|
| Data processing |
Primary sequencing data that produced by Illumina HiSeq 2500 , called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Reads preprocessing，mapping and CITS analysis with raw data followed CLIP Tool Kit pubulished in the article named CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
Genome build: mm10
processed data files format and content: bed
|
| |
|
| Submission date |
Mar 21, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
Hongyu Lin |
| E-mail(s) |
helly147@163.com
|
| Phone |
008613070178987
|
| Organization name |
Zhejiang University School of Medicine
|
| Street address |
Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Xihu District
|
| City |
hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE112175 |
The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response |
|
| Relations |
| BioSample |
SAMN08768727 |
| SRA |
SRX3829236 |
