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. Overall design: 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.