ChIPseq-on-Chip Droplet-Microarray as a miniaturized high throughput platform for parallel ChIP-seq experiments

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Chromatin immunoprecipitation (ChIP) in combination with sequencing (ChIP-seq) is used for investigation of protein-DNA interactions in vitro and based on direct sequencing of DNA fragments of interest obtained by ChIP via next generation sequencing (NGS). ChIP-seq technology is widely used to fundamentally assess chromatin structure and function, as well as to design and develop new epigenetic drugs. Scaling down ChIP experiments and developing platforms to carry out simultaneous ChIP reactions are becoming a popular trend, because it is important to minimize the experiment's duration and cost. The current platforms rely either on the microtiter plate format and associated with large reaction volumes and initial cell numbers, or on the microfluidic principle not yet compatible with high-throughput. We recently developed a miniaturized platform for live cell high-throughput screening based on superhydrophilic-superhydrophobic (SL-SH) patterning called Droplet-Microarray (DMA). The DMA platform enables the screening of hundreds to thousands of factors on a standard microscope slide format in volumes ranging from 3 to 80 nL. Such screens can be made in parallel without the need to pipet each individual spot. Here I propose to adapt the DMA platform to conduct high-throughput ChIP-seq experiments starting initially with as few as 100 to 1000 live cells. The main goal of this project is to develop and optimize protocols for highly parallel ChIP-seq on the DMA platform. In addition, this novel methodology will be evaluated for high-throughput applications via proof-of-concept screening on DMA. In this case cells will be introduced to different stimuli on the DMA platform and parallel ChIP-seq analysis will take place in the droplets themselves to distinguish between the final epigenetic states in treated cell populations. Utilizing the DMA platform for high-throughput ChIP reactions is superior to current technologies because it enables a dramatic reduction in reaction volumes while ensuring higher throughput DMA technology also has the potential to combine high throughput screening (introducing cells to a compound library) and ChiP analysis as a read-out performed in a single droplet, a procedure that is impossible when working with any of the current platforms.