RNA Sequencing of Nalm-6 SF3B1 K700E MT and Nalm-6 SF3B1 WT cells

SF3B1, a core component of the spliceosome involved in branch point recognition and 3' splice site selection is frequently mutated in hematopoietic malignancies. Though its associations with clinical outcomes are unclear, mice and zebra fish with conditional SF3B1 knock-in mutations develop macrocytic anemia. A hallmark of SF3B1 mutation is an increase to cryptic 3' splice site (C3SS) usage, a finding that is recapitulated across multiple isogenic and patient cell types. Mechanisms contributing to cryptic splice site choice and the influence of mis-splicing on posttranscriptional isoform regulation in SF3B1 mutants remains unclear. Our data indicate that SF3B1 K700E mutant Nalm-6 cells carry a significantly different set of cryptic 3' splice sites than ones utilized in wild type cells. Overall design: RNA-Seq was performed to compare the alternative splicing differences between Nalm-6 SF3B1 mutant and Nalm-6 SF3B1 wild type cells. Three technical replicates were performed for SF3B1 K700E cells and three technical replicates for SF3B1 wild type cells.