We have developed a highly multiplexed quantitative ChIP-seq technology (hmqChIP-Seq) as a powerful platform allowing to assay a comprehensive set of epigenetic markers (namely histone posttranslational modifications (hPTMs) and other marks including and beyond DNA methylation). With our platform hmqChIP-Seq, 96 or more drug conditions can be screened against 24 or more epigenetic modification markers, such as histone or DNA PTMs using specific antibodies and next-generation sequencing readout.
The highly multiplexed library is sequenced at a very low depth (<50 000 reads per sample, equivalent to <100 Mio reads for a 96×24 dataset) for quantifying global marker levels, making the assay highly cost effective unlike in a normal ChIP-Seq experiment. Through a novel patented selection/amplification strategy, hmqChIP-Seq can be further used to quantify multiple select genomic loci (target: 24 loci) that could e.g., represent important tumour suppressor or stress response genes. Analysing scarce sequencing information still allows accurate quantification of the global and locus-specific level of each marker under each condition. One multiplexed workflow with 96 conditions and 24 antibodies can hence provide the same global quantification as 96×24=2304 quantitative western blots, and, through multiplexed selection of target loci, and equivalent of 96x24x24=55 296 ChIP-qPCR reactions.