|
| Status |
Public on May 24, 2022 |
| Title |
HL60.m6A.Rep2.Input |
| Sample type |
SRA |
| |
|
| Source name |
human neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HL-60 neutrophil-like cells
genotype: Wild-type
treatment: Infection with Escherichia coli
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from neutrophils with TRIzol reagent (Invitrogen) then subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit (61006, Invitrogen) following the manufacturer’s instructions. For m6A-immunoprecipitation (IP) samples, RNA fragmentation and immunoprecipitated of m6A-containing RNA fragments via anti-m6A antibody (202003, Synaptic System) were performed.
The input mRNA sample (Input) and purified mRNA sample (m6A-IP) were prepared for library construction and sequencing using standard Illumina protocols
m6A-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The adapters and low quality bases were removed
The Fastq files were aligned to the reference genome (hg38) using Hisat2 (v2.1.0)
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Assembly: hg38
Supplementary files format and content: txt
|
| |
|
| Submission date |
Apr 19, 2022 |
| Last update date |
May 24, 2022 |
| Contact name |
Yang Liu |
| E-mail(s) |
yliu@immunol.org
|
| Organization name |
Peking Union Medical College&Chinese Academy of Medical Sciences
|
| Department |
Immunology
|
| Street address |
Dongdan Santiao 5
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE201060 |
Transcriptome-wide m6A Methylation Profiling of dHL-60 human neutrophils by m6A-seq |
|
| Relations |
| BioSample |
SAMN27642038 |
| SRA |
SRX14918175 |
