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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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Updated: Jan 15, 2026

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

Comparative Transcriptomic Profiling of Corneal Compartments Using Single-Cell and Single-Nucleus Sequencing.

Hongran Zhao^1,2,3, Xiaoyu Li^1,2, Xiaowen Zhang^1,2,3

¹Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China.

Investigative Ophthalmology & Visual Science

|October 8, 2025

Summary

Single-cell RNA sequencing (scRNA-seq) provides better corneal epithelial cell differentiation insights, while single-nucleus RNA sequencing (snRNA-seq) excels at identifying corneal endothelial cells. This guides optimal transcriptomic study strategies.

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Last Updated: Jan 15, 2026

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

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

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

Published on: March 12, 2021

Area of Science:

Ophthalmology
Genomics
Molecular Biology

Background:

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) are powerful tools for corneal transcriptomics.
Challenges in corneal cell isolation and platform-specific cell-type distribution can lead to misinterpretations.

Purpose of the Study:

To establish cell-type-specific recommendations for corneal transcriptomics using scRNA-seq and snRNA-seq.
To objectively evaluate the performance of scRNA-seq and snRNA-seq across different corneal cell types.

Main Methods:

Systematic evaluation of scRNA-seq and snRNA-seq performance using matched human and mouse corneal datasets.
Immunofluorescence validation of Col8a1 and Kdr gene expression.

Main Results:

scRNA-seq demonstrated superior prediction of corneal epithelial cell differentiation trajectory.
scRNA-seq captured more stromal keratocytes and associated disease genes.
snRNA-seq was more effective for identifying and characterizing corneal endothelial cells.

Conclusions:

scRNA-seq and snRNA-seq offer complementary strengths for corneal transcriptomics.
Findings provide practical guidance for selecting optimal sequencing strategies based on research needs.