Enzyme-free digital counting of endogenous circular RNA molecules in Formalin-Fixed Paraffin-Embedded tissues from patients with B-cell malignancies

Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies. We quantified circular RNA expression by total RNA sequencing of four different Mantle Cell Lymphoma cell lines, REC-1, Granta-519, Z138 and UPN2 and the Multiple Myeloma cell line, H929. Overall design: High quality RNA samples were depleted for ribosomal RNA and sequenced on a HiSeq 4000 from Illumina, no replicates were done. CircRNA quantification was done using the bioinformatics algorithms known as Find_circ and CIRI2. The data was used for designing a panel of NanoString assays for specific circRNAs