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Fig. 6 | Genome Biology

Fig. 6

From: Insights into the design and interpretation of iCLIP experiments

Fig. 6

Constrained cDNA-ends affect the cDNA-starts at 3′ splice sites. a The cDNA-starts (solid lines) and cDNA-ends (dotted lines) of U2AF2-iCLIP are plotted around intron-exon junctions (position 0 being the first nucleotide of the exon). cDNAs are divided into three length categories: 17–29 nt, 30–34 nt and 35-39 nt; the distribution of all cDNAs together is shown in grey. b Same as (a), but using only cDNAs that end in the intron. c Same as (a), but using only cDNAs that end in the exon. d Same as (a), but showing PTBP1-iCLIP1 cDNA-starts (full lines) and cDNA-ends (dotted lines). e Same as (a), but showing PTBP1-iCLIP2 (using 4SU and optimised RNase conditions) cDNA-starts (full lines) and cDNA-ends (dotted lines). f Same as (a), but showing PTBP1-iCLIP3 (omitting 3′ dephosphorylation) cDNA-starts (full lines) and cDNA-ends (dotted lines). g The composition of genomic nucleotides around iCLIP cDNA-ends from PTBP1-iCLIP1. h Same as (g), but showing PTBP1-iCLIP2. i Same as (g), but showing PTBP1-iCLIP3. j Proportions of cDNAs that map to introns which contain cDNA-ends at positions overlapping the last two nucleotides of introns. PTBP1-iCLIP1 and PTBP1-iCLIP2 are compared to PTBP1-iCLIP3 iCLIP, which was performed without using PNK to dephosphorylate RNAs in step 2. This enriches for RNAs that contain a 3′ OH, which can occur when they are cleaved at their 3′ end independently of RNase I, such as the 3′ ends of intron lariats

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