Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

We apply geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology, to investigate the heterogeneous nature of suprachiasmatic nucleus (SCN) in adult mouse. The 3D quantitative data enables spatial gene expression pattern visualization . The dataset identified genes that are coexpressed in a specific region, mark domains of similar global pattern of expression, and can be used for mapping the position of single cells dissociated from adult SCN. In laser capture microdissection (LCM), hexagon grids with 40-μm maximal radius was used and the transcriptome of each hexagon was obtained using single-cell RNA-seq technology.