Ultra-high Throughout Single Cell Multi-omic Analysis of Histone Modifications and Transcriptome in Mouse and Human Brains

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Histone modification carries rich epigenetic information that constitutes a mechanism of cellular memory. Single cell analysis of histone modification in conjunction with transcriptome could help uncover this critical layer of cellular memory and lead to better definition of cell types and states in the brain. Here, we propose to develop an ultra-high throughput method, known as Paired-Tag, for joint profiling of histone modifications and transcriptome in single cells. In preliminary studies, we have demonstrated the feasibility and utility of this method by applying it to the adult mouse frontal cortex and hippocampus. In the proposed research, we will further develop and optimize Paired-Tag to enable automation and support large-scale data production project. Additionally, we will implement a series of quantitative QC metrics to benchmark the performance of the new Paired-Tag procedure against existing Paired-Tag procedures. We will then use the optimized experimental procedure to generate adult mouse brain cell atlas of histone modifications and transcriptome at single cell resolution. We will additionally characterize the dynamic changes in histone modifications and transcriptome at single cell resolution in the mouse brain across multiple developmental stages. Finally, to demonstrate proof of principle of Paired-Tag for analysis of human brains, we will use it to assay the prefrontal cortex (BA46) in adult human brains from 3 males and 3 females.