Differentially expressed miRNAs are identified in primary CD34⁺ CML cells. (A) DESeq2 analysis of differentially expressed miRNAs in CD34⁺ cells, comparing 3 NBM and 6 CML samples (3 IM responders and 3 IM nonresponders). Plots show the distribution of differentially expressed miRNAs, representing the fold-change between CML relative to NBM (left panel). Red dots represent the differentially expressed miRNAs with adjusted P values < .05. G plots package was used to plot heat maps, accompanied with unsupervised dendrogram analysis, based on the differentially expressed miRNAs with adjusted P values < .05 (right panel). (B) Similar analyses performed for miRNAs found to be differentially expressed between IM responders (R) and IM nonresponders (NR). (C) Differentially expressed miRNAs were determined using a TaqMan qPCR microfluidics device on extracts of CD34⁺ cells obtained from NBM (n = 11) and CML samples (n = 22). Raw Ct values obtained from the 96-well multiplexing microfluidics device were organized using the HTqPCR package and normalized using the quantile method with the limma package. A nonparametric Mann-Whitney U test was performed to compare unpaired samples. Levels of 20 of the miRNAs tested were shown to be different between CD34⁺ NBM and CML cells. Data points represent quantile-normalized Ct values relative to CD34⁺ NBM cells. All comparisons shown are statistically significant (Benjamini-Hochberg-adjusted P value < .05).