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. 2020 Sep;26(9):1216–1233. doi: 10.1261/rna.074856.120

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© 2020 Patton et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 4. — xRIPiT-seq and CLIP-seq are robust and comparable approaches to identify CASC3 binding sites. (A) A meta-exon plot showing xRIPiT and CLIP read counts in the 150 nt window at exon ends. Read normalization was carried out as in Figure 3A. (B) Comparison of gene-level CASC3 read density (RPKM_IP-seq) in xRIPiT (diamonds) and CLIP (triangles) for canonical (darker-shaded shapes) and noncanonical regions (lighter-shaded shapes), and for intronless genes (empty shapes). Gene binning and error bars are as in Figure 3B. (C) Comparison of the linear fit coefficients (or intercepts, in log space) of the six classes in B. Classes are labeled on the bottom. (D) Percentage of all canonical EJC regions where read depth is greater than or equal to twofold as compared to intronless gene read counts in the indicated data sets. (E) Venn diagram showing counts of canonical regions from the top 20% expressed genes where CASC3 footprint read depth in nRIPiT, xRIPiT and CLIP is greater than or equal to twofold as compared to intronless gene read counts.