PARE analysis identifies SOX-specific cut sites in endogenous RNAs.

A) Number of peaks/cut sites identified specifically in SOX or GFP samples. B) Fraction of the peaks identified in SOX or GFP samples that were detected in both biological replicates (“shared peaks”), relative to the maximum distance allowed between the peaks. C) Correlation plot of the heights of peaks found in both SOX+ samples. Peak height is defined as the highest read count within the peak window, at the position defined as the putative cut site. D) Position of the cut sites found in both replicates (“shared cut sites”) within the mRNAs relative to the length of the transcript. E) Position of the shared cut sites relative to the coding region of the mRNA (in all samples > 90% of the peaks fall within coding transcripts). ND = not determined, because multiple transcript isoforms are present in the annotation and the cut site position would differ between isoforms. NA = no coding sequence annotated. F) Position of shared cut sites relative to annotated landmarks on transcripts. For all panels in this figure, a scanning window of 4 nt, a multiplicative factor of 4, a confidence level of 99.99%, were used to predict cut sites. All cuts sites ≤ 5 nt apart in the two replicates were used for the analyses in panel C-F (SOX-specific peaks: n = 456, GFP-specific peaks: n = 84).