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Updated: Oct 29, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Generating and Using Transcriptomically Based Retinal Cell Atlases.

Karthik Shekhar¹, Joshua R Sanes²

¹Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; and California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, USA;

Annual Review of Vision Science

|July 6, 2021

Summary

This summary is machine-generated.

High-throughput single-cell RNA sequencing (scRNA-seq) reveals diverse retinal cell types across vertebrates. This technology aids research into retinal development, disease, and evolution, expanding to the entire brain.

Keywords:

Müller glia amacrine cell bipolar cell horizontal cell photoreceptor retinal ganglion cell

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Area of Science:

Neuroscience
Genomics
Cell Biology

Background:

Retinal cell organization is conserved across vertebrates.
Classifying diverse retinal cell types has been challenging until recently.
High-throughput single-cell RNA sequencing (scRNA-seq) offers new possibilities.

Purpose of the Study:

To review the experimental and computational aspects of scRNA-seq for retinal cell atlasing.
To highlight studies using scRNA-seq to create vertebrate retinal cell atlases.
To discuss the applications of these atlases in understanding retinal function and evolution.

Main Methods:

Single-cell RNA sequencing (scRNA-seq) for high-throughput analysis.
Computational methods for analyzing scRNA-seq data.
Comparative studies across multiple vertebrate species.

Main Results:

Development of comprehensive retinal cell atlases in several vertebrate species.
Identification and classification of numerous retinal cell types.
Enabled studies on retinal development, injury response, disease genes, and cell-type evolution.

Conclusions:

scRNA-seq is a powerful tool for dissecting retinal cell diversity.
Retinal atlases provide insights into retinal function, dysfunction, and evolution.
The approach is expanding to study the entire eye and brain visual centers.