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Fig. 5 | Genome Biology

Fig. 5

From: Insights into the design and interpretation of iCLIP experiments

Fig. 5

Non-coinciding cDNA-starts are required to map the crosslink sites within Y-tracts. a The cDNA-starts of PTBP1-iCLIP1 and CLIP experiments are plotted around the ends of >35 nt Y-tracts that are annotated as T-rich or TC-rich low-complexity sequence in the human genome (hg19). cDNAs of PTBP1-iCLIP1 are divided into four length categories: 17–29 nt, 30–34 nt, 35–39 nt and >39 nt. b Same as (a), but using U2AF2-iCLIP and CLIP cDNAs. c Same as (a), but showing the positions of cDNA-ends. d Same as (b), but showing the positions of cDNA-ends. e Heatmap showing the coverage of PTBP1-binding motifs at the PTBP1-iCLIP1, PTBP1-iCLIP2, PTBP1-eCLIP or PTBP1-irCLIP crosslink clusters that were defined with a 3-nt clustering window. Each row shows the average coverage for 300 clusters of similar length, sorted from shortest to longest clusters. The white line marks the nucleotide preceding the start and the nucleotide following the median end of all clusters that were combined in each row. A colour key for the coverage per nucleotide of the PTBP1-binding motifs is shown on the right

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