|
| Status |
Public on Sep 20, 2023 |
| Title |
notaddDrug_2, ip |
| Sample type |
SRA |
| |
|
| Source name |
PANC-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC-1
cell type: Human PDAC cell lines
genotype: not Cytochalasin D treatment
treatment: m6A
|
| Treatment protocol |
Purified RNA 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 from cell lines was isolated by using Trizol reagent (Invitrogen). The RNA samples were quantified by measuring absorbance at 260 nm with a UV spectrophotometer, and only analytes with an RNA integrity number (RIN) ≥ 7.0 were used in further experiments.
|
| 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
notaddDrug_2, ip
|
| Data processing |
Clean reads were mapped the hg19 genome using STAR
MACS2 were used to identify peaks
Peaks from each sample were merged to a set of union peaks using BEDTools merge.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: m6A-seq
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Sep 20, 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) |
| GSE211588 |
CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer [m6A-seq] |
| GSE211589 |
CFL1-induced super enhancer RNA m6A modification promotes local chromatin accessibility and oncogenes transcription in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN35803699 |
| SRA |
SRX20728657 |
