Simultaneously spatiotemporal gene expression and chromatin accessibility for mouse brain development

Brain are complex biological tissues which function relies on coordinated anatomical and molecular structure comprised by a large number of specialized cells. The spatial architecture of brain which is key to the understanding of its physiological and pathological significance is formed during embryo development. However, the molecular basis for discrete neuroanatomical domains particularly in the context of spatial organization of the brain is inadequate. Here, we introduced Spatial-ATAC-RNA-seq by crisscross indexing (SPARC-seq), a method for parallel profiling of gene expression and chromatin accessibility with spatial information retained in developing mouse brain. Our study has established a direct means to spatially determine the coordination between chromatin accessibility and transcriptome, identified the chromatin potential to define cell fate determination of brain structure, and uncovered spatiotemporal regulatory principles during mammalian brain development.