|
| Status |
Public on Nov 01, 2023 |
| Title |
PDAC cells, sgiPaf1-2, Paf1 KD Chromatin RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic ductal adenocarcinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pancreatic ductal adenocarcinoma cells
genotype: Paf1 knockdown
|
| Treatment protocol |
The cells were treated with 1μg/mL doxycycline to induce dCas9-KRAB expression
|
| Growth protocol |
The PDAC cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual.
500ng RNA of each sample was used to prepare libraries. RNA libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NR603).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The paired-end reads were trimmed and quality check were carried out using trim-galore (version 0.6.4)
Trimmed reads were aligned to the mouse genome (GRCm38.p6) from GENCODE using STAR(v.2.7.7a)
Reads in BAM files were counted using featureCounts(v.2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts numbers of all samples generated by featureCounts
|
| |
|
| Submission date |
Nov 10, 2022 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Xiangzheng Liu |
| E-mail(s) |
lxz19@mails.tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Street address |
Tsinghua University, Haidian District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE217742 |
Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation III |
| GSE217745 |
Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression |
|
| Relations |
| BioSample |
SAMN31684208 |
| SRA |
SRX18233038 |
