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. 2009 Sep 28;4(9):e7192. doi: 10.1371/journal.pone.0007192

Figure 2. Computationally-predicted microRNAs.

Figure 2

A. Example SHRiMP alignment of small RNA sequences, shown here as grayscale “wiggle” tracks on the genome browser, were used to predict a potential microRNA structure. One track is shown for each chromosomal strand. For the miRDeep-predicted microRNA track, the dashed line represents the predicted mature microRNA sequence (aligning with the most frequent small RNA sequence from the wiggle tracks) and the solid line represents the remaining predicted hairpin precursor. B. Table showing numbers of predicted microRNAs produced by miRDeep based on small RNAs derived from ESC or NSC and those subtracted by overlap with the sno/miRNA track, the RNA genes track, or the RepeatMasker track of the genome browser. The remaining predictions shown at bottom constitute an aggregated group of 818 predicted microRNAs. C. Venn diagram showing distinct known (top) and predicted (bottom) microRNAs derived by miRDeep from ESC or NSC cultures as well as the numbers in common between the two conditions. Fewer predicted microRNAs were identified as common to ESC and NSC than known microRNAs. D. ChIP-Seq read densities derived from H9 ESC cultures [41] flanking the aggregated start positions for H1 ESC predicted microRNA precursors. See legend for color specific to each modified histone mark. E. ChIP-seq read densities derived from H9 ESC cultures flanking the aggregated start positions for H1 NSC predicted microRNA precursors.