RNA sequencing of wild-type and mutant KRAS human lung cancer cell lines with of without FASN inhibition.

The goal of this study is to compare the RNA-seq derived transcriptome of mutant KRAS and wild-type KRAS lung cancer cell lines under fatty acid synthase (FASN) inhibition. We extracted total RNA with TRIzol from cells treated with 0.2 µM TVB-3664 (FASN inhibitor) or 0.2% DMSO for 4 days. One µg of total DNAse-treated RNA was used for library. cDNA was ligated to adapters and PCR amplified. Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina NextSeq 500. Reads were aligned to the human hg38 reference genome. Only uniquely mapped reads were retained for further analyses. Gencode annotation for human (version v37) was used as reference alignment annotation and downstream quantification. Gene level expression was calculated using featureCount (v2.0.1) using intersection-strict mode by exon. Counts were calculated based on protein-coding genes from the annotation file. Low expressed genes were filtered using a per time-point approach with RPKM >= 0.5 in all samples in one or the other group. Overall design: We extracted total RNA from 2 mutant KRAS (H460 and A549) and 2 wild-type KRAS (H522 and H661) human lung cancer cell lines treated with 0.2 µM TVB-3664 or 0.2% DMSO for 4 days