Gunaratne et al. BMC Genomics 2011, 12:277 http://www.biomedcentral.com/1471-2164/12/277 A. TaqMan Page 7 of 14 B. Illumina Figure 3 Analysis of miRNAs produced at the tgu-mir-2954 locus. TaqMan and Illumina RNA-seq data generated from independent sets of birds (n = 6 in each data set) for expression from the tgu-mir-2954 locus. A) TaqMan results, where the relative gene expression of each individual bird (open circle) was obtained by using the 2^-ddCt method [98]; the relative gene expression of either Silence (white bar) or Song (gray bar) group was the mean of six individuals; the P value was calculated by paired t test since each song stimulated animal was explicitly paired with a silence control animal collected simultaneously. B) Read counts from the Illumina RNA-seq for miR-2954-3p and miR-2954-5p (also shown in the Additional File 1, Table S4).