A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines
Nikki R. Kong, Li Chai, Daniel G. Tenen, Mahmoud A. Bassal
Abstract
chromatin profiling technique that enables high-resolution chromatin mapping and probing. Herein, we describe our adapted CUT&RUN protocol for transcription factors (TFs). Our protocol outlines all necessary steps for TF profiling including the procedure to obtain proteinA-Mnase, while also outlining the bioinformatic pipeline steps required to process, analyze, and identify novel binding sites and sequences. Due to the small number of cells required, this method will allow the elucidation of cell context-dependent functions of many TFs. For details on the use and execution of this protocol, please refer to Kong et al. (2021).
Topics & Concepts
Computational biologyComputer scienceTranscription factorChromatinProfiling (computer programming)Pipeline (software)Protocol (science)BiologyGeneGeneticsProgramming languageMedicineAlternative medicinePathologyGenomics and Chromatin DynamicsRNA Research and SplicingRNA and protein synthesis mechanisms