Whole genome expression after modulation of miR-30a expression. Same transfections described in Figure 2 were done before transcriptome analyses. A. Strategy for identification of potential miR-30a targets. As shown, no significant differences were found between miR-30a-KD and control miR-159-KD cells. Therefore, downstream analyses focused on the Pre-miR-30a conditions. B. Scatter plot comparing Pre-miR-30a to miR-159-KD control condition. From 227 significant genes in this comparison, 86 were downregulated, 36 of which contained a miR-30a seed sequence. C. Validation of a subset of these 36 genes was done with qRT-PCR (see also Additional file 4: Figure S3). Gene expression values are relative to HPRT1 housekeeping gene. P values (for comparisons to control miR-159 KD) under 0.05 are represented with an asterisk (*). D. Target validation was done after cloning 3′UTR sequences of AVEN and FOXD1 into a luciferase reporter plasmid and transfection of MCF7 cells. P value under 0.05 (two-tailed student t test) is represented with a (*).
Ouzounova et al. BMC Genomics 2013 14:139 doi:10.1186/1471-2164-14-139