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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
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

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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