|
Status |
Public on Jan 29, 2024 |
Title |
#7_Resistant |
Sample type |
SRA |
|
|
Source name |
Primary cell lines derived from pancreatic cancer of a genetically engineered mouse model
|
Organism |
Mus musculus |
Characteristics |
tissue: Pancreas genotype: Ptf1awt/Cre;Kraswt/LSL-G12D;Trp53loxP/loxP group: Resistant
|
Treatment protocol |
To induce resistance, cells were treated with increasing doses of trametinib (LKT) until they grew in 100x of their IC50. One batch was cultivated with 100x IC50 of trametinib in the culture medium (termed resistant ) with medium exchange every 2-3 days on a regular basis. Another batch of each cell line was kept under drug withdrawal and samples were named according their passage number in drug-free medium (P5 and P12)
|
Growth protocol |
DMEM high-glucose medium containing 10% fetal bovine serum, 1% penicillin/streptomycin and 1% non-essential amino acids
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega) according to manufacturer’s instruction. TruSeq Stranded mRNA Kit (Illumina) with 100 ng input RNA
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
MEKi resistant #7_Resistant
|
Data processing |
Demultiplexing of the sequencing reads with Illumina CASAVA v. 2.17 or bcl2fastq 2.19 Adapter trimming using Skewer v. 0.1.116 or 0.2.2 Quasi-mapping with salmon v. 0.12 Converting transcript-level counts to gene-level counts and performing of differentially gene expression analysis using DESeq2 v.1.18 Genome_build: mm10 Supplementary_files_format_and_content: csv files of normalized read counts and differential gene expression analysis results
|
|
|
Submission date |
Mar 04, 2020 |
Last update date |
Jan 29, 2024 |
Contact name |
Laura Godfrey |
E-mail(s) |
l.godfrey@dkfz-heidelberg.de
|
Organization name |
DKTK Partner Site Essen/Düsseldorf
|
Street address |
Hufelandstraße 55
|
City |
Essen |
ZIP/Postal code |
45147 |
Country |
Germany |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE146348 |
Multi-omics characterization of MEK inhibitor resistant pancreatic cancer based on a genetically engineered mouse model-derived in vitro system |
|
Relations |
BioSample |
SAMN14290168 |
SRA |
SRX7847325 |