What are the limitations of ChIP?

There are several disadvantages of using ChIP technology. The primary drawbacks are access and cost. CHiP-chip techniques cost approximately 400-800 USD per array, while ChIP-seq costs 1000-2000 USD per lane. ChIP is also a time consuming process, and typically requires 20-40 million reads per library for sufficient signaling over background. ChIP also exhibits high background and/or low variable yields as compared with controls, leading to inconclusive data. Additionally, the quality of ChIP-Seq data relies on the quality of the antibody. Validating antibody quality can be a laborious and time consuming process.