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Spatial organization of the mouse retina at single cell resolution by MERFISH

Jongsu Choi, Jin Li, Salma Ferdous, Qingnan Liang, Jeffrey R. Moffitt and Rui Chen (ruichen@bcm.edu)
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Jongsu Choi: Baylor College of Medicine
Jin Li: Baylor College of Medicine
Salma Ferdous: Baylor College of Medicine
Qingnan Liang: Baylor College of Medicine
Jeffrey R. Moffitt: Program in Cellular and Molecular Medicine, Boston Children’s Hospital; Department of Microbiology, Harvard Medical School
Rui Chen: Baylor College of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing 8 previously unknown displaced amacrine cell subtypes and establishing the connection between the molecular classification of many cell subtypes and their spatial arrangement. Furthermore, we identified spatially dependent differential gene expression between subtypes, suggesting the possibility of functional tuning of neuronal types based on location.

Date: 2023
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DOI: 10.1038/s41467-023-40674-3

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