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Table 1 Deletions in CLIP, iCLIP and mRNA-seq cDNAs

From: Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Experiments

Unique cDNAs

Unique cDNAs with deletions in sequence reads

Unique cDNAs with deletions (1 to 25 nucleotides)

Proportiona

Nova CLIP

3,852,778

482,871

421,417

11%

Ago mRNA CLIP

1,105,217

79,126

61,211

5.5%

mRNA-Seq

4,857,809

60,110

18,936

0.4%

Nova iCLIP

166,330

6,174

3,749

2.3%

hnRNP C iCLIP

698,046

17,412

8,923

1.3%

TIA1 iCLIP

991,158

6,945

6,261

0.6%

TIAL1 iCLIP

2,786,090

12,011

10,963

0.4%

TDP-43 iCLIP

3,506,515

97,708

48,138

1.4%

  1. aProportion was defined as the percentage of (Unique cDNAs with deletions (1 to 25 nucleotides)/Unique cDNAs).