Constructing a Spatially Resolved Single-cell Atlas of the Mouse Retina with the MERSCOPE Platform

The retina is the light-sensing part of the visual system and is composed of six neuron types and several non-neuronal cell types, with an estimated over 100 subtypes exist based on cell morphology, function, and molecular markers. Recent single-cell transcriptomic studies show that most cell subtypes in the mouse retina can be identified based on their transcriptome. Furthermore, cell subtypes defined by their transcriptome correlated well to results obtained from morphology and function. However, a major drawback of current single-cell transcriptome technologies is that they require the isolation of single cells, resulting in the loss of spatial information. Unfortunately, spatial information is critical for studying of many biological processes, such as characterizing neuron circuit, development, and degeneration. Thus, to gain a thorough understanding of the mechanism of retinal function, construction of a spatially resolved single-cell atlas of the retina is essential. We performed single-cell spatial transcriptomic profiling on the mouse retina with MERFISH using Vizgen’s MERSCOPETM Platform. Cell organization of the retina has a distinct feature where many cell subtypes are organized in a compact area. As a result, to generate the spatial map of the retina, it is necessary to optimize the procedure. For example: 1) Due to the compactness of the retina, a new protocol needs to be developed that allows antibody staining against cell membrane along with MERFISH probes against transcripts to improve cell segmentation; 2) Cell segmentation algorithm needs to be trained and optimized for the retina; 3) As some of the cell subtypes are extremely rare (<0.01% of cell population in the retina), a novel cell annotation strategy leveraging the single-cell transcriptomic map is essential. Over 60K cells have been profiled with MERFISH. We will discuss how all cell types and most subtypes can be successfully identified and placed on the retinal spatial map.

 

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