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Histone modifications play an essential role in chromatin-associated processes including gene regulation and epigenetic inheritance. It is therefore very important to quantitatively analyze histone modifications at both the single gene and whole genome level. Here, we describe a robust chromatin immunoprecipitation (ChIP) method for
Arabidopsis
, which could be adapted for other plant species. This method is compatible with multiple downstream applications including q
PCR
, tilling arrays, and high-throughput sequencing.