|
| Status |
Public on Apr 29, 2019 |
| Title |
m6A-seq_IP_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Monomac-6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Monomac-6
cell type: acute monocytic leukemia
tissue: peripheral blood
antibody: m6A antibody
treatment: DMSO
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocols (Dan et al., 2012)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: m6A-seq
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the hg38 genome assembly using Tophat 2.1.1
peaks were called using MACS2 and exomePeak.
the m6A peaks were annotated using an ad hoc perl script.
GSEA and DAVID tool were used to perform pathway enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization
|
| |
|
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianjun Chen |
| E-mail(s) |
jianchen@coh.org
|
| Phone |
6262185591
|
| Organization name |
Beckman Research Institute of City of Hope
|
| Department |
Systems Biology
|
| Lab |
Chen Lab
|
| Street address |
1218 S. 5th Ave., Room 2062
|
| City |
Monrovia |
| State/province |
CA |
| ZIP/Postal code |
91016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE103496 |
Sequencing of mRNA with N6-methyladenosine (m6A) modification in AML cells upon DMSO or FTO inhibitor treatment |
| GSE103497 |
RNA-seq and m6A-seq of AML cells with FTO knockdown or inhibition |
|
| Relations |
| BioSample |
SAMN07605617 |
| SRA |
SRX3161623 |
