Spatial Organization of the Mouse Retina at Single Cell Resolution by MERFISH

Authors

Jongsu Choi
Jin Li
Salma Ferdous
Qingnan Liang
Jeffrey R Moffitt
Rui Chen

Publication Date

8-15-2023

Journal

Nature Communications

DOI

10.1038/s41467-023-40674-3

PMID

37582959

PMCID

PMC10427710

PubMedCentral® Posted Date

8-15-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

no

Keywords

Animals, Mice, Gene Expression Profiling, In Situ Hybridization, Fluorescence, Retina, Amacrine Cells, Single-Cell Analysis

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.

Comments

This article has been corrected. See Nat Commun. 2023 Sep 28;14:6057.

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