|
| Status |
Public on Jun 01, 2024 |
| Title |
SLAMseq_CB6644_MYC_ER_OHT_R2 |
| Sample type |
SRA |
| |
|
| Source name |
NA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: NA
cell line: KPC
cell type: pancreatic ductal adenocarcinoma
genotype: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, MYC-ER
treatment: 200 nM 4-OHT 4 h
|
| Treatment protocol |
KPC-AID-Ruvbl1 cells were treated with 1 µM 5-Ph-IAA for 3 or 15 h respectively followed by 2 h of labelling with 800 µM 4sU. KPC-MYC-ER cells were treated with 1 µM CB-6644 for 20 h followed by 4 h treatment with 4-OHT and 2 h of labelling with 400 µM 4sU.
|
| Growth protocol |
KPC-AID-Ruvbl1 and KPC-MYC-ER cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted using miRNeasy kit (Qiagen)
QuantSeq 3' mRNA-Seq Library Prep Kit (FWD)
OTHER: SLAMseq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
GRAND SLAM (version 2.0.5g, Jürges et al., 2018, Bioinformatics)
Trimming of 5' 10 nt UMI, and 3' Adapter
STAR alignment to the mm10 reference sequence
Differential gene expression analysis using DESeq2 (version 1.36.0)
Assembly: mm10
Supplementary files format and content: .tsv/.csv file containing the results of differential gene expression analysis
|
| |
|
| Submission date |
Oct 19, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Elmar Wolf |
| E-mail(s) |
elmar.wolf@biozentrum.uni-wuerzburg.de
|
| Organization name |
Biocenter of the University of Würzburg
|
| Department |
Department of Molecular Biology and Biochemistry
|
| Lab |
Cancer Systems Biology Lab
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| State/province |
Bavaria |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE216092 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 (SLAM-Seq) |
| GSE216095 |
Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 |
|
| Relations |
| BioSample |
SAMN31367038 |
| SRA |
SRX17955630 |
