Uncovering the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines
Illumina miRNA-seq method to uncover the expression profile of NSCLC in-vitro experimental models consisting of cell lines A549, H460 compared to healthy BEAS-2B cell line, and lung tissue (NSCLC and paired normal) from urethane treated 6-week-old FVB/NJ mice. We aimed to uncover the divergent epigenetic background of KRAS-mutant NSCLC in mouse and human cell lines, extensively used as biological models in relevant research. To that end, we have comprehensively mapped the functional miRNA and lncRNA landscape of human (A549 and H460) and mouse (experimentally developed LUAD) NSCLC models and correlated current results with LRF/ZBTB7A expression Overall design: Total RNA was extracted from cell lines and mice and library preparation was performed by QIAseq miRNA library kit. Adapters were ligated to 3' and 5' ends of miRNAs and subsequently, universal cDNA synthesis reaction with Unique Molecular Indices (UMI) assignment, cDNA cleanup, library amplification and library cleanup, were performed. Downstream RNA sequencing reactions were performed in Illumina iSeq 100 instrument (Illumina, Inc., US) in single-ended mode with 75 bp sequence length and total reads ranging from 1.0 to 1.5 million per sample.