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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: Dec 9, 2025

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

Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis.

Andrew P Voigt¹, S Scott Whitmore¹, Nicholas D Lessing¹

¹Departments of Ophthalmology and Visual Sciences, the University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA; Institute for Vision Research, the University of Iowa, Iowa City, IA, 52242, USA.

Experimental Eye Research

|September 10, 2020

Summary

This summary is machine-generated.

Spectacle is a new web tool making ocular single-cell RNA sequencing data accessible. It helps researchers easily find gene expression patterns in eye tissues without complex bioinformatics.

Keywords:

Choroid Gene expression Interactive RPE Retina Single-cell RNA sequencing

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Area of Science:

Ophthalmology
Genomics
Bioinformatics

Background:

Single-cell RNA sequencing (scRNA-seq) advances ocular gene expression research.
Identifying rare cell types and expression changes in ocular tissues is crucial.
Sharing and analyzing scRNA-seq data presents computational challenges for many researchers.

Purpose of the Study:

To develop an accessible, interactive web-based resource for exploring ocular scRNA-seq data.
To reduce the bioinformatics barrier for researchers studying ocular gene expression.
To facilitate the identification of cell types expressing specific genes in ocular tissues.

Main Methods:

Development of Spectacle, a web resource powered by the R package cellcuratoR.
Utilizing the Shiny framework in R for interactive data visualization.
Pre-processing and integration of five ocular scRNA-seq datasets.

Main Results:

Spectacle provides interactive exploration of ocular scRNA-seq data.
Users can identify cell-specific gene expression and transcriptomic subpopulations.
Flexible differential expression analyses are readily available through the platform.

Conclusions:

Spectacle democratizes access to complex ocular scRNA-seq datasets.
The tool simplifies the identification of gene expression patterns in ocular tissues.
It empowers researchers without extensive computational expertise to analyze scRNA-seq data.