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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Dec 4, 2025

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Published on: May 22, 2017

An optimized protocol for retina single-cell RNA sequencing.

Benjamin R Fadl¹, Seth A Brodie², Michael Malasky²

¹Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD.

Molecular Vision

|October 22, 2020

Summary

This summary is machine-generated.

This study presents a gentle method for preparing mouse retinal samples for single-cell RNA sequencing (scRNA-seq). The optimized protocol and data analysis enhance transcriptional complexity and data quality for robust retinal research.

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Last Updated: Dec 4, 2025

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Published on: May 22, 2017

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

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Published on: March 12, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

Neuroscience
Genomics
Molecular Biology

Background:

Single-cell RNA sequencing (scRNA-seq) is crucial for understanding gene expression at the cellular level.
High-quality sample preparation is vital for accurate transcriptome data analysis.
Retinal sample preparation for scRNA-seq requires specific optimization to preserve native expression profiles.

Purpose of the Study:

To develop and validate a gentle, rapid, and optimal dissociation protocol for mouse retinal samples for scRNA-seq.
To improve the quality of scRNA-seq data obtained from retinal tissues.
To assess the impact of fresh versus frozen retinas on cell or nuclei suspensions for scRNA-seq.

Main Methods:

Modified dissociation conditions for mouse retina preparation.
Incorporated additional filtering steps in the computational pipeline for data analysis.
Evaluated fresh versus frozen retinal tissues for scRNA-seq.

Main Results:

A gentle dissociation method was established, minimizing cell death and preserving cell morphology.
The protocol led to the detection of higher transcriptional complexity.
An improved computational pipeline resulted in better quality scRNA-seq data from retinal samples.
Advantages and limitations of using fresh versus frozen retinas were demonstrated.

Conclusions:

A simple, robust, and reproducible protocol for retinal scRNA-seq analysis was developed.
This protocol is particularly beneficial for comparative studies in retinal research.
The optimized method ensures high-quality data for advancing our understanding of retinal biology.