Chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) is increasingly used to study protein-chromatin interactions or local epigenetic modifications at genome-wide scale. ChIP-seq can be performed directly with several ng of immunoprecipitated DNA, which is generally obtained from a several million cells, depending on the quality of the antibody. ChIP-seq can only provide binding/modification information for a single epitope but multidimensional analyses require often information about the coordinate binding of several factors to, and/or corresponding epigenetic modification of targets sites. To this aim sequential ChIP assays (reChIP) can in principle be combined with massive parallel sequencing but the low yields associated to such approach have seriously hampered widespread application. The present protocol couples a linear DNA amplification (LinDA) step to reChIP assays, thus facilitating global studies by using the LinDA-reChIP-seq protocol.

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