Figure 1

Overview of the miRNA sequencing data and validation of selected miRNAs. (A) The heat-map shows the log2 fold change ratios between minus (induced) and plus doxycycline conditions. Expression values are log counts per millions +2 pseudo-counts after normalization with TMM (weighted trimmed mean of M-values) in the edgeR package. Euclidian distance and average linkage method were used to generate the clusters of miRNAs using the gplots package in R. There are 28 miRNAs in the clustering of which 10 are downregulated, while 18 are upregulated. There is generally good agreement between the replicate samples in the experiments. (B) Correlation between sequencing and qPCR results. Comparison is done with log2 fold change (FC) and ΔΔCq for all the relevant comparisons between +/− dox. Grey diagonal line indicates a slope of 1, while the blue line is the fit to the data. The slope of the fit is 1.14 and highly significant, indicating a very strong correlation between the platforms. The two points on the top of the blot are miR-221 and miR-222, which deviate from the ideal slope due to a greater increase seen in qPCR than in sequencing. (C) Comparison of sequencing and qPCR data for miR-221-3p (Ci), miR-22-3p (Cii) and miR-503-5p (Ciii). Values are the same as those used in (B).