Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Lı Wang, Zhuxia Li, Qingmei Shen, Minhan Wang, Fangfang Qu, Guizhong Cui, Kai Chen, Guangdun Peng
Abstract
The brain is a complex tissue whose function relies on coordinated anatomical and molecular features. However, the molecular annotation of the spatial organization of the brain is currently insufficient. Here, we describe microfluidic indexing-based spatial assay for transposase-accessible chromatin and RNA-sequencing (MISAR-seq), a method for spatially resolved joint profiling of chromatin accessibility and gene expression. By applying MISAR-seq to the developing mouse brain, we study tissue organization and spatiotemporal regulatory logics during mouse brain development. MISAR-seq combines spatial-ATAC-seq and RNA-seq for spatial profiling of both chromatin accessibility and gene expression, as demonstrated in the developing mouse brain.