|
| Status |
Public on Jun 08, 2023 |
| Title |
PANC-1, GEMIN5, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PANC-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC-1
cell type: PDAC cells
rip antibody: GEMIN5
|
| Treatment protocol |
Cell lysate was then sonicated, digested with DNase I and RNase I for 15 min at 37 °C and incubated with Dynabeads protein A/G (Millipore) conjugated with anti-GEMIN5 antibody overnight at 4 °C.
|
| Growth protocol |
After treatment with 4-thiouridine (200 µM) for 14 h, PANC-1 cells were subjected to UV crosslinking and lysed on ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After end repair using T4 PNK (NEB), the bead-antibody-RNA complexes were treated with proteinase K, and the bound RNA was purified by acidic phenol/chloroform extraction and ethanol precipitation.
For PAR-CLIP sequencing, the purified RNAs were utilized for library construction using the NEBNext small RNA library prep kit (E7330S) and sequenced on an Illumina HiSeq4000
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were mapped to the hg38 human genome by Bowtie2 followed by removing adapters and removing low-quality reads by fastp
CLIP-seq peaks were identified using Piranha
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
IGV was used to visualize the binding sites of GEMIN5.
Assembly: hg38
Supplementary files format and content: bigWig
|
| |
|
| 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 |
GPL20301 |
| Series (2) |
| GSE206967 |
N6-methyladenosine-enhanced FZR1 translation contributes to gemcitabine insensitivity in pancreatic cancer via quiescence maintenance [PAR-CLIP-Seq] |
| GSE206969 |
N6-methyladenosine modification of FZR1 mRNA promotes gemcitabine resistance in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN29362341 |
| SRA |
SRX15901419 |
