To overcome some of these limitations and enhance the utility of ChIP, it can be combined with other techniques:
ChIP-seq: Combining ChIP with high-throughput sequencing (ChIP-seq) allows for genome-wide analysis of protein-DNA interactions with greater resolution. ChIP-chip: Combining ChIP with microarrays (ChIP-chip) enables the examination of protein-DNA interactions across specific genomic regions or the entire genome. qPCR: Quantitative PCR (qPCR) can be used following ChIP to quantify the amount of DNA associated with the protein of interest at specific genomic locations.
