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Fig. 2 | Genome Biology

Fig. 2

From: Insights into the design and interpretation of iCLIP experiments

Fig. 2

Crosslink-associated (CL)-motifs are enriched at cDNA deletions and cDNA-starts in iCLIP. a Proportion of eIF4A3 cDNAs with deletion at each position relative to the cDNA-start. Only cDNAs shorter than 40 nt are examined. b Analysis of all PTBP1 experiments examined in this study shows the proportion of cDNAs from each experiment that overlap with a CL-motif at each position relative to the cDNA-start. c Proportion of eIF4A3-CLIP3 cDNAs that overlap with a CL-motif at each position relative to the cDNA-start. Only cDNAs shorter than 40 nt are examined; they are divided into those lacking deletions or containing a deletion within the first 7 nt or anywhere in the remaining portion of the cDNA. d The cDNAs of eIF4A3-CLIP3 containing a deletion within the first 7 nt are further sub-divided into three categories. First, cDNAs with CL-motifs between the 1st and 10th nucleotide of the cDNA. Second, the remaining cDNAs that contain CL-motifs at the position 0. And third, all remaining cDNAs. The proportion of cDNAs that overlap with a CL-motif at each position relative to the cDNA-start is then plotted for each sub-category. e Proportion of PTBP1-iCLIP2 cDNAs that overlap with a CL-motif at each position relative to the cDNA-start. Only cDNAs shorter than 40 nt are examined and are divided into those lacking T-to-C transitions or containing a transition within the first 7 nt or anywhere in the remaining portion of the cDNA. f The cDNAs of PTBP1-iCLIP2 containing a T-to-C transition within the first 7 nt are further sub-divided into three categories. First, cDNAs with CL-motifs overlapping the position 0. Second, the remaining cDNAs that contain CL-motifs between the 1st and 10th nucleotide of the cDNA. And third, all remaining cDNAs. Visualisation as in (d). g Same as (c), but for PTBP1-iCLIP1. h Same as (d), but for PTBP1-iCLIP1

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