GSE120677
Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes
Very long intergenic non-coding RNAs (vlincRNAs) are a novel class of long transcripts (~50 kb to 1 Mb) with cell type- or cancer-specific expression. We report the discovery and characterization of 256 vlincRNAs from a cohort of 64 primary childhood pre-B and pre-T acute lymphoblastic leukemia (cALL) samples, of which 61% are novel and specifically expressed in cALL.  Validation was performed in 35 pre-B and pre-T cALL primary samples. We show that their expression is cALL immunophenotype and molecular subtype-specific and correlated with epigenetic modifications on their promoters, much like protein-coding genes. While the biological functions of these vlincRNAs's are still unknown, our results suggest they could play a role in cALL etiology or progression. Please note that the study consists of investigating very long intergenic non coding RNAs (vlincRNAs) in childhood acute lymphoblastic leukemia. The study primarily uses RNA-seq data (GSE89071) with the current additional epigenetic data that is specific to this study (chip-seq and wgb-seq). Overall design: Identification and characterization of very long intergenic non-coding RNAs in childhood ALL Please note that the 'characteristic: cell type' field indicates the cell type of each sample. The cell type is 'Pre-B' cells, and the cALL subtype is also indicated. For the control, CD10+ and CD19+ cord blood cells were used.