|
| Status |
Public on Jun 08, 2023 |
| Title |
BXPC-3,GEM-SEN, INPUT |
| Sample type |
SRA |
| |
|
| Source name |
BXPC-3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BXPC-3
cell type: PDAC cells
phenotype: GEM-SEN
rip antibody: none
|
| Treatment protocol |
Purified mRNA was fragmented and incubated with anti-m6A antibody (Synaptic Systems, 202003)-conjugated beads in RIP reaction buffer overnight at 4 °C
After incubation, the bound RNAs were purified via proteinase K treatment, acidic phenol/chloroform extraction and ethanol precipitation
|
| Growth protocol |
total RNA extracted from cell lines was treated with DNase I to eliminate DNA and purified to mRNA using poly-T oligo-attached magnetic beads.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One tenth of the fragmented RNA served as an input control in RNA sequencing.
RNA fragments from the m6A-IP and input samples were used for cDNA library preparation and sequenced on an Illumina HiSeqX Ten PE150 platform.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The input reads were trimmed to the same length as the m6A-IP reads using fastx_trimmer from FASTX-Toolkit.
Clean reads were mapped to the hg38 genome using STAR. MACS2 and MeTPeak were used to call peaks, and the cut-off P value for a significant peak for MACS2 was 1e-6.
Only m6A peaks identified by both peak-calling methods were retained and merged using BEDTools. The human annotation file (GENCODE v27) from the GENCODE database was used to perform the m6A annotation. Homer was used to search the motif enriched in m6A peaks.
The read coverage in m6A-IP and input of each peak were calculated using Multicov from BEDTools with RPKM for normalization (reads per kilobase million). The ratio of m6A-IP RPKM to input RPKM was used to calculate the enrichment of each m6A peak.
Differentially modified m6As with a P value of < 0.05 and the absolute value of fold change of > 1.5 were treated as differentially methylated m6As.
Assembly: hg38
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Jun 27, 2022 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Rui Li |
| E-mail(s) |
lirui@sysucc.org.cn
|
| Organization name |
Sun Yat-sen University Cancer Center
|
| Street address |
651 Dongfeng East Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE206968 |
N6-methyladenosine-enhanced FZR1 translation contributes to gemcitabine insensitivity in pancreatic cancer via quiescence maintenance [m6A-seq] |
| GSE206969 |
N6-methyladenosine modification of FZR1 mRNA promotes gemcitabine resistance in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN29362348 |
| SRA |
SRX15901479 |
