Generation of KRAS knockout pancreatic cancer cell line PANC1
Data files
Jan 16, 2024 version files 2.02 MB
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PANC1.xlsx
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README.md
Abstract
We used CRISPR to inactivate mutant KRAS and STAT3 in PANC1 (KRASG12D) pancreatic cancer cell line. Gene expression analysis of KRAS intact vs. knockout cells identified sets of genes involved in protein synthesis, cell differentiation, and metabolic processes, while the expression of MAPK/ERK target genes remained unperturbed.
README: PANC1 pancreatic cancer cell line
https://doi.org/10.5061/dryad.5hqbzkhct
We used CRISPR to inactivate mutant KRAS and STAT3 in PANC1 (KRASG12D) pancreatic cancer cell line. Gene expression analysis of KRAS intact vs. knockout cells identified sets of genes involved in protein synthesis, cell differentiation, and metabolic processes, while the expression of MAPK/ERK target genes remained unperturbed.
Methods
Cell line construction
For CRISPR/Cas9-mediated knockouts, we used sgRNAs specific for KRAS and STAT3. Knockout efficiency was measured by Western blotting. Multiple technical replicates were obtained for each CRISPR targeted gene. Genomic DNA from clonal cell lines was collected using QiaAmp DNA Mini Kit (Qiagen). PCR products for sequencing were amplified using Taq DNA polymerase (Invitrogen) and cloned into a pBluescript vector. At least 10-15 bacterial colonies were sequenced per cell line. For RNA isolation, cells were harvested with TRIzol reagent (Invitrogen). Cells were maintained in DME medium supplemented with 5% fetal bovine serum (FBS).
RNA sequencing
RNA sequencing of tumor cells with basic bioinformatics and statistical analyses were performed by Novogene Corp. The FPKM counts represent fragments per kilobase of transcript per million mapped reads.
Funding
National Cancer Institute
Description of the data and file structure
Data are presented in FPKM format. Data include parental intact (Pa1), KRAS knockout (PaKKO), STAT3 knockout (PaSTAT3KO), and KRAS/STAT3 double knockout derivatives (PaDKO).