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Sample GSM3059340 Query DataSets for GSM3059340
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´╝îmapping 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
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
BioSample SAMN08768727
SRA SRX3829236

Supplementary file Size Download File type/resource
GSM3059340_L9-RIG-I.bed.gz 53.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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