GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3583900 Query DataSets for GSM3583900
Status Public on Mar 12, 2019
Title UV-RIP-seq 8h
Sample type SRA
Source name RAW264.7 cells
Organism Mus musculus
Characteristics cell line: RAW264.7 cells
cell type: murine macrophage cell line
passages: 15-18
strain: C57BL/6
rip antibody: flag-tag (Millipore, MAB3118,clone 2EL-1B11 )
infection: VSV infection for 8 hr
Treatment protocol RAW264.7 cells stably expressing Flag-tagged TRIM25 were mock treated with PBS or VSV infection for 8 hr and were subjected to crosslinking with 0.3 J/cm2 of 254 nm UV light in a crosslinker HL-2000 (UVP). RIP experiment was performed using anti-Flag antibody, and then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing.
Growth protocol RAW264.7 cells stably expressing Flag-tagged TRIM25 were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).
Extracted molecule total RNA
Extraction protocol RIP experiment was performed according to the manufacturer’s instructions. The isolated RNA was further assessed by RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model HiSeq X Ten
Data processing Primary sequencing data that produced by Illumina Xten, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by scripts.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into mm10 transcripts was processed by Stringtie.
Differential expression analysis between sample 1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: isoforms.fpkm_tracking
Submission date Jan 30, 2019
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 GPL21273
Series (1)
GSE112175 The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response
BioSample SAMN10845770
SRA SRX5310523

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap