Extended Data Fig. 9: Features of the 5′ end signals of Cleave-seq.
From: Alternative polyadenylation by sequential activation of distal and proximal PolyA sites
a, UCSC genome browser view of the 5′ end signals of polyA+ RNA from Cleave-seq on DGCR8 gene. The zoom-in view of the 20 nt region flanking the Drosha cleavage site (left dotted) is shown in the dotted box on the right (* marks the 5′ end base). b, Upset plot of the identified cleavage sites from 4 Cleave-seq libraries. Only the peaks found in at least 2 samples were included. For the 654 genes with longer 3′UTR enriched in NM, the number of peaks located in the downstream 10 nt window of their pPAS and dPAS are shown in the upper right box. c, Violin plot depicting the ratio of the number of Cleave-seq reads in the 10 nt window downstream pPAS over that of dPAS (n = 160). The dotted grey line represents 10-fold ratio. The red line represents the median. The lower and upper hinges of the box plots correspond to the first and third quartiles (the 25th and 75th percentiles). The p-value was determined using the two-sided Wilcoxon test.