Illuminating Biology with Spatially Resolved, Single-cell Transcriptomics

Biological systems are comprised of numerous cell types, intricately organized to form functional tissues and organs. Cell atlas initiatives with single-cell RNA sequencing have begun to characterize cell types based on their RNA expression profiles. However, the tissue organization is lost when cells are dissociated for single-cell sequencing, making it difficult to study how the cellular heterogeneity is contributing to the function of the tissue. Multiplexed error robust in situ hybridization (MERFISH) technology  enables the direct profiling of the spatial organization of intact tissue with genomic-scale throughput. Through combinatorial labeling, sequential imaging, and error-robust barcoding, MERFISH technology provides the highest detection efficiency and resolution available for spatial genomics. In a single experiment, hundreds of thousands of cells can be spatially profiled with subcellular resolution with high accuracy and reproducibility. In this presentation, we used the technology to profile gene expression in situ across large tissue areas in mouse brain and human colon cancer, discover and map cell types in complex tissue in response to external stimuli in animal models, and analyze the intracellular organization of transcriptome with sub-cellular resolution in individual cells.

Learning Objectives:

1. Learn about the benefits of spatially resolved, single-cell transcriptomics for further characterizing cell types based on their RNA expression profiles.

2. Learn about different research applications of MERFISH technology for the direct profiling of the spatial organization of intact tissues with genome-scale throughput.