mRNA profiles of CD43++c-kit+, CD43+c-kit- and CD43-c-Kit- AML1-ETO9a murine leukemic bone marrow cells

We discovered a spontaneous differentiation path characterized by CD43 and c-Kit in the AE9a murine model, where the leukemia-initiating potential is lost while leukemic cells display features of erythroid maturation. Therefore, we sorted out CD43++c-Kit+, CD43+c-Kit- and CD43-c-Kit- AE9a leukemic cells for RNA-sequencing analyses to determine the underlying transcriptome. Overall design: CD43++c-Kit+, CD43+c-Kit- and CD43-c-Kit- AML1-ETO9a murine leukemic bone marrow cells were sorted out. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays.