Genome-wide analysis of p53 binding by ChIP-seq

We used ChIP-seq to identify the genomic locations bound by p53 in mouse kidney Snap-frozen kidney was crosslinked with formaldehyde to generate a snap shot of all protein-DNA interactions occurring in the nucleus at that particular point in time, then antibodies were used to immunoprecipitate the p53 protein together with crosslinked DNA fragments. Following reversal of crosslinks and digestion of protein, adaptors were ligated to immunoprecipitated DNA and PCR was used to generate clonally amplified amplicons before sequencing by synthesis using the Illumina Solexa Genome Analyzer.