Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq

Two sets of 10 samples from patients with CMML were used for this study. The first set (CMML11 to CMML20) includes 10 blood samples supplied by Eric Jourdan (Biological Resource Center CHU-Nimes, France). Peripheral blood mononuclear cells were separated by Ficoll-Hypaque density gradient and preserved in RNA Later. The second set (CMML1 to CMML10), delivered by Eric Solary (Gustave Roussy Institut) consisted of 10 samples from Bone marrow or peripheral blood separated on Fycoll-Hypaque. CD14+ monocytes were then sorted from PBMCs with magnetic beads and the AutoMacs system as previously described by Merlevede et al. (2016). RNA-seq experiments were performed on the twenty samples described above and libraries have been prepared using the “TruSeq Stranded Total RNA Gold” Kit from Illumina. Whole genome sequencing was performed on 1 CMML (sample 10) using the Illumina TruSeq DNA PCR-Free Library Preparation Kit. RNA-Seq full length sequencing were performed on 2 CMMLs (samples 7 and 13) : converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech) and sequenced with the SQK-PBK004 kit (PCR Barcoding kit) on MinION sequencer from Oxford Nanopore Technologies.