Homo sapiens Raw sequence reads

HITS-CLIP experiments provide the state-of-the-art means of identifying RNA-binding sites for typical and atypical RNA binding proteins (RBPs) in living cells, which are crucial for understanding the increasingly recognized complexity of RNA regulation. However, current CLIP technology was limited to small amounts of CLIP RNA and complicate procedures with high experimental failure rates. Here we describe an easy-operating CLIP (eoCLIP) protocol. While maintaining high quality and precision, eoCLIP omits the RNA radioactive labeling by 32P and the followed autoradiographic visualization steps. It also applied the commercially available small RNA library preparation kit to simplify the efficiency of RBP-bound RNA recovery. By incorporating paired IgG as a crucial control, eoCLIP improves signal-to-noise in identifying authentic binding sites. The easy-operation and efficiency of the eoCLIP protocol offers a unique opportunity for large-scale generation of transcriptome-wide binding maps for RBPs.