Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

There has been an extensive effort underway to profile epigenetic features at the genome-wide scale using primary ex vivo tissues. Cell-type specificity of epigenomes calls for enrichment to obtain a homogenous cell population from a small quantity of tissues. Thus technologies that permit both ultralow input and high throughput are desired for profiling an array of histone marks. Here we demonstrate a simple microfluidic technology, SurfaceChIP-seq, for profiling genome-wide histone modifications using as few as 30 cells per assay and with up to 8 assays running in parallel. We applied the technology to study epigenomic landscapes in neurons and glia in prefrontal cortex and cerebellum of mouse brain. The data revealed extensive epigenomic difference in the two regions on important functional elements such as promoters and enhancers. We examined genome-wide H3K4me3 and H3K27me3 profiles in GM12878 cell line (using 30 to 10k cells per assay) using SurfaceChIP-seq. They include data generated by 4-channel (4C) and 8-channel (8C) devices and also devices produced using (3-Aminopropyl) triethoxysilane /Glutaraldehyde/Protein A (AGP) linker. We also profiled H3K4me3, H3K27ac and H3K27me3 marks in neurons (NeuN+) and glia (NeuN-) from mouse cerebellum and prefronal cortex (using 100 or 1k nuclei per assay) using SufaceChIP-seq. We generated RNA-seq data on neurons and glia from mouse prefronal cortex and cerebellum. Finally, we also included SurfaceChIP-seq and RNA-seq data obtained using the homogenate of mouse prefrontal cortex and cerebellum (referred to as "mix" in their file names). Three mice (M1, M2 and M3) were used in the study.