|
| 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 |
| 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 |
GPL21273 |
| Series (1) |
| GSE112175 |
The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response |
|
| Relations |
| BioSample |
SAMN10845770 |
| SRA |
SRX5310523 |
