The significance of different algorithms in transcriptome analysis of leukemic cells with rearranged MLL (gene expression)

This study shows how the way by which the RNA-Seq data is analyzed affects the resulting gene expression profile. Three parameters were explored: the RNA-Seq analysis algorithm pipeline (cufflinks – Cuffdiff 2 or HTSeq & DESeq), sequencing depth and sequencing protocol: single or paired end, 100 or 50 bases. For comparison, the same samples were processed by gene microarrays. RNA-Seq and gene microarray were conducted on total RNA from four acute lymphoblastic leukemia (ALL) precursor B cell lines, two lines carrying the chromosome translocation t(4;11) in which the human MLL gene is rearranged, and two lines lacking this abnormality.