Microfluidic low-input fluidized-bed enabled ChIP-seq device for automated and parallel analysis of histone modifications

Genome-wide epigenetic changes such as histone modifications form a critical layer of gene regulations and have been implicated in a number of different disorders such as cancer and inflammation. Progress has made to decrease the input required for gold-standard genome-wide profiling tools like chromatin immunoprecipitation followed by next generation sequencing (i.e. ChIP-seq) to allow scarce primary tissues of specific type from patients and lab animals to be tested. However, there has been very little effort to rapidly increase the throughput of these low-input tools. In this report, we demonstrate LIFE-ChIP-seq (Low-Input Fluidized-bed Enabled Chromatin Immunoprecipitation combined with sequencing), an automated and high-throughput microfluidic platform capable of running multiple sets of ChIP assays in as little as 1 h with as few as 50 cells per assay. Our technology will enable testing of a large number of samples and replicates with low-abundance primary samples in the context of precision medicine. We examined genome-wide H3K4me3 profiles of GM12878 cell line starting with 1000 cells down to as few as 50 cells per assay. The ChIP experiment was performed using an automated microfluidic device (LIFE-ChIP), which performed 4 replicate experiments in every run under the same operating conditions. We also demonstrated that the device was capable of profiling two histone marks (H3K4me3 and H3K27ac) in one run with two replicates on each mark. The file name contains information on "cell number per assay"_"loading volume in microliters"_"washing time in minutes"_"no. of chamber"_"no. of device/histone mark (in the case of two marks being tested)". For example, "300_120L_20W_C1_H3K4me3" refers to the dataset taken by having 300 cells per assay, using 120 microliters of loading volume, 20 min of washing per buffer, and chamber 1 for characterizing H3K4me3 among the two histone marks profiled in the same run.