Transcriptome profiling of 60 human lung cell lines by strand-specific RNA sequencing after rRNA depletion. Transcriptome profiling of 60 human lung cell lines by strand-specific RNA sequencing after rRNA depletion

We performed deep RNA sequencing of 60 human lung cell lines: 50 lung adenocarcinoma cell lines, 7 NSCLC (non small cell lung cancer, non-adenocarcinoma) cell lines, 3 non-transformed lung cell lines. Total RNA was isolated and subjected to rRNA depletion to maintain also non-polyadenylated transcripts. Strand-specific next generation sequencing (NGS) using Illumina HiSeq allowed us to distinguish reads in the sense and antisense direction. The cell lines were sequenced in 2 or 3 replicates. Reads were aligned to the human reference genome GRCh38 using STAR mapper. The expression of 58,096 genes was calculated in terms of FPKM for every sample. Overall design: Gene expression profiling of NSCLC lung cancer cell line panel