|
| Status |
Public on Apr 27, 2021 |
| Title |
Cov2-M3_IP |
| Sample type |
SRA |
| |
|
| Source name |
SARS-CoV-2 viral infected METTL3 KD (M3) Caco-2 cells
|
| Organisms |
Homo sapiens; Severe acute respiratory syndrome coronavirus 2 |
| Characteristics |
cell line: Human colorectal adenocarcinoma Caco-2 cells
genotype: METTL3 KD
infection: SARS-CoV-2 virus
passages: P2
viral strain: Betacoronavirus
merip antibody: anti-m6A polyclonal antibody (ab151230, abcam)
|
| Treatment protocol |
Infected with SARS-CoV-2
|
| Growth protocol |
The human colorectal adenocarcinoma Caco-2 cells were purchased from ATCC. Caco-2 cells were cultured in high-glucose MEM (Thermo Fisher Scientific) supplemented with 20% fetal bovine serum (FBS; Gibco), MEM NEAA (Thermo Fisher Scientific) and 50 U/ml penicillin-streptomycin (Gibco) in a humidified 5% CO2 atmosphere. For SARS-CoV-2 live cell infection, SARS-CoV-2 isolate USA-WA1/2020 was obtained from BEI Resources. SARS-CoV-2 virus was propagated, and infectious units were quantified by plaque assay using Vero E6 cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from infected METTL3 KD (M3) Caco-2 cells were extracted and purified for IP of MeRIP-Seq
RNAs were extracted from viral infected-Vero or Caco-2 cells by TRIzol /TRIzol LS and Direct-zol RNA Kit (Zymo). The RNAs were treated with DNaseI, concentrated and quantified.
Total RNA, the immunoprecipitated m6A- containing RNAs and the input RNAs were processed for library generation by TruSeq mRNA library prep kit (Illumina).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to the SARS-CoV-2 (NC_045512.2) genome or hg38 genome assembly using STAR or Bowtie2 aligner
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called by MACS2 using the following configuration: p-value< 0.05, call-summit, keep-dup 1 --nomodel --extsize 200 or keep-dup all --nomodel --extsize 200 for SARS-CoV-2 alignment; p<1e-5, -keep-dup auto --extsize 200 nomodel for human alignment
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: SARS-CoV-2 (NC_045512.2), GRCh38, ChlSab1.1
Supplementary_files_format_and_content: xlsx: contains normailzed gene expression by DESeq2; bigBed: contains peaks detecting by MACS2 (1: keep-dup 1; all: keep-dup all)
|
| |
|
| Submission date |
Feb 19, 2021 |
| Last update date |
Apr 27, 2021 |
| Contact name |
Na Li |
| E-mail(s) |
nal023@health.ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Pediatrics
|
| Lab |
Tariq Rana's Lab
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL29320 |
| Series (1) |
| GSE167075 |
m6A modification in SARS-CoV-2 virus regulates host cell innate immune response |
|
| Relations |
| BioSample |
SAMN17983527 |
| SRA |
SRX10131027 |
