The chart highlights steps of various representative CLIP-seq protocols. Not all steps are included. XL, UV cross-link; IP, immunopurification; phosphatase, removal of 3′ phosphate; kinase, addition of 5′ phosphate; RT, reverse transcription; L3, 3′ adaptor ligation to RNA or DNA; L5, 5′ adaptor ligation; PK extraction, proteinase K extraction from nitrocellulose membrane; Ppt/column, alcohol precipitation or column cleanup of nucleic acid; TBE, Tris-borate-EDTA; SA, streptavidin.