Chromatin immunoprecipitation followed by next-generation sequencing analysis 
(ChIP-Seq) is a powerful method with which to investigate the genome-wide 
distribution of chromatin-binding proteins and histone modifications in any 
genome with a known sequence. The application of this technique to a variety of 
developmental and differentiation systems has provided global views of the 
cis-regulatory elements, transcription factor function and epigenetic processes 
involved in the control of gene transcription. Here we describe several 
technical aspects of the ChIP-Seq assay that diminish bias and background noise 
and allow the consistent generation of high-quality data.