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Sample GSM4378634 Query DataSets for GSM4378634
Status Public on Jan 29, 2024
Title #3_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
#3_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 SAMN14290178
SRA SRX7847315

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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