miRNA expression in the rat lung after irradiation. (A) Unsupervised hierarchical clustering of differentially expressed miRNAs in early (3w), middle (12w) and late (26w) stages of RILI. Red indicates higher expression and green indicates lower expression in irradiated lungs. Black means no expression difference. (B) Overlaps of co-regulated miRNAs (>2.0 fold) across various post-irradiation time courses. Data shown are real numbers of up-regulated (Up) and down-regulated (Down) miRNAs. The numbers in the overlapped areas represent the number of differentially transcribed miRNAs shared by two or three groups. (C, D) qRT-PCR and microarray results of miRNA (Rno-miR-21and Rno-Let-7i) expression level at each post-irradiation time point. Results are expressed as relative quantifications (RQ) of the miRNA expression level in each sample relative to non-irradiated controls, and normalized to U6 snRNA. Each reaction was performed in triplicate and the average CT was used for RQ calculation. *p < 0.05, in 2-tailed student’s t test when compared to non-irradiated controls.