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Sample GSM7468777 Query DataSets for GSM7468777
Status Public on Jun 09, 2023
Title RNAseq of FC1242 PT (replicate 2)
Sample type SRA
 
Source name FC1242
Organism Mus musculus
Characteristics cell line: FC1242
cell type: Pancreatic cancer cell
treatment: untreated
Treatment protocol Cells were left untreated or treated with 60 nM MRTX1133 for 24 hours.
Growth protocol Parental human SUIT2 or mouse Fc1242 cells and MRTXR human SUIT2 or mouse Fc1242 cells were cultured in 10 cm dishes in duplicate.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted Nucleospin® RNA isolation kit (Macherey-Nagel GmbH & Co.) following the manufacturer’s instructions.
PolyA-enriched RNA libraries were prepared according to manufacturer's protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description FC1242_RNAseq.txt
Data processing Quality control of the raw fastq files was performed using the software tool FastQC
Sequencing reads were trimmed with Trimmomatic and aligned using the STAR aligner
Read quantification was performed with RSEM
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis
lowly expressed genes—those not having counts per million (cpm) at least 3 in at least 3 of the samples—were filtered out and then trimmed mean of M-values (TMM)10 normalization was applied.
Assembly: GRCh38 for human and GRCm38 for mouse
Supplementary files format and content: SUIT2_RNAseq.txt (tab delimited txt file with nomalized counts)
Supplementary files format and content: FC1242_RNAseq.txt (tab delimited txt file with nomalized counts)
 
Submission date Jun 08, 2023
Last update date Jun 24, 2023
Contact name Herve Tiriac
E-mail(s) htiriac@health.ucsd.edu
Phone 8582465564
Organization name UCSD Health
Department Surgery
Street address 3855 Health Sciences Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL21273
Series (1)
GSE234449 Dual inhibition of KRASG12D and pan-ERBB is synergistic in pancreatic ductal adenocarcinoma
Relations
BioSample SAMN35674933
SRA SRX20638803

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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