Fig. 3.

Purification of RNA oligomers and DNA amplimers after the CLIP procedure. (a) Autoradiograph of the ³²P-labeled RNA oligonucleotides with various sizes isolated as described in the text and subsequently ligated to the RA3 and RA5 adapters using the Illumina’s TruSeq small RNA prep kit (Subheading 3.11). The box indicates radioactive RNA with the ligated adapters (RNA + adapters) that is extracted to produce the CLIP DNA library. Shown are sizes in nucleotides of the radioactively labeled low-molecular-weight DNA ladder (DNA ladder, right) and approximate mobilities of the xylene cyanol (XC) and bromophenol blue (BPB, left). (b) Representative fluorescent image of ethidium bromide-stained native PAGE of the CLIP library (Subheading 3.14). The box indicates the region of the final CLIP library that was extracted from the gel. Lanes are the custom RNA ladder (CRL), CLIP library, and high-resolution ladder (HRL). Ladder fragment sizes are indicated in base pairs. Please note that the theoretical size of a PCR product without an insert is 117 bp