|
| Status |
Public on Apr 20, 2024 |
| Title |
PANC-1 cells, YBX1 IP-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreas
cell line: PANC-1
cell type: Pancreatic cancer cells
treatment: pretreated with CAFs-derived Evs
rip antibody: YBX1 antibody
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PANC-1 cells were pretreated with CAF-deirved Evs. Pretreated cells were UV-crosslinked (at 254nm, 400 mJ/cm2) and lysed with RIP lysis buffer. Lysed pellets were sonicated and treated with RNaseI (Life Technologies) Turbo DNase (Life Technologies). Then magnetic beads coated with 1 μg of YBX1 antibody were added into cell lysate and incubated overnight at 4 °C. The precipitated RNA was released with proteinase K and extracted 2 times with phenol chloroform isoamyl alcohol, followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE.
Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Novaseq sequencer according to the manufacturer’s recommended protocol.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to human reference genome (UCSC hg19) using bowtie2 software (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).
Assembly: UCSC HG19
Supplementary files format and content: Excel file of the peak calling
|
| |
|
| Submission date |
Apr 17, 2024 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Chonghui Hu |
| E-mail(s) |
huchonghui@gdph.org.cn
|
| Organization name |
Guangdong Provincial People’s Hospital
|
| Street address |
NA Zhongshan 2nd Road, Guangzhou
|
| City |
Guangzhou |
| ZIP/Postal code |
5100080 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE264220 |
RIP sequencing in PANC-1 cells to map the YBX1-binding mRNA of PANC-1 cells treated with CAF-derived Evs |
|
| Relations |
| BioSample |
SAMN40995295 |
| SRA |
SRX24288471 |
