|
| Status |
Public on Apr 26, 2018 |
| Title |
UV-RIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW264.7
cell type: macrophage cell line
passages: 15-18
strain/background: C57BL/6
infection: VSV for 12 hr
rip antibody: Flag-tag (Millipore, MAB3118, clone 2EL-1B11)
|
| Treatment protocol |
RAW264.7 cells stably expressing Flag-tagged RIG-I were treated with VSV 4-SU at 100μM for 12hr and crosslinked with UV at 365 nm for 300 mJ/cm2. 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 RIG-I were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
UV-RIP was performed with anti-Flag antibody. 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 |
Illumina HiSeq 4000 |
| |
|
| Description |
Sample 2
RAW264.7 cells upon VSV infection for 12 hr.
Processed data file: 3-10.txt
|
| Data processing |
Primary sequencing data produced by Illumina HiSeq 4000, 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 Trimmomatic and Fastx-toolkit.
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 lncmm10 transcripts was processed by Stringtie.
Differential expression analysis between sample1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
Oct 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Minghong Jiang |
| E-mail(s) |
jiangminghong@163.com
|
| Organization name |
Chinese Academy of Medical Sciences
|
| Street address |
5 Dong Dan San Tiao
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE106254 |
Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response |
|
| Relations |
| BioSample |
SAMN07839987 |
| SRA |
SRX3338847 |
