Acquisition and transcriptomic analysis of tissue micro-regions using a capillary-based method

Profiling the site-specific transcriptomes of microregions of interest (mROIs) contributes to a complete understanding of multicellular organisms. However, the simple and efficient isolation of mROIs for spatially detecting gene expression remains challenging. Here, we develop an efficient capillary-based microdissection system (CMS) for precisely isolating targeted samples from tissue sections. Optimized sampling procedures reveal that CMS can perform mROI isolation with an efficiency of 97.9 %, and detect a sufficient number of genes for gene expression profiling (CMS-seq). We apply CMS-seq to uncover spatial heterogeneity in the cortex region of the mouse, and the subregions of hippocampus in an Alzheimer's disease (AD) mouse. Results demonstrate that CMS-seq can profile spatial transcriptomes in tissue sections and holds promise for application spatial multi-omics.