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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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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq.

Jinzhou Yuan¹, Peter A Sims^1,2,3

¹Department of Systems Biology, Columbia University Medical Center, New York, NY 10032 USA.

Scientific Reports

|September 28, 2016

Summary

This study introduces an automated microwell array platform for single-cell RNA sequencing, improving efficiency and reducing contamination. The system successfully profiled thousands of cells, revealing gene expression heterogeneity in glioma neurospheres.

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Area of Science:

Single-cell genomics
Microfluidics
Molecular biology

Background:

Single-cell RNA sequencing (scRNA-Seq) enables comprehensive gene expression profiling from complex tissues.
Microwell arrays offer a scalable microfluidic platform for single-cell analysis with high capture efficiency and imaging compatibility.

Purpose of the Study:

To develop and validate an automated microwell array platform for enhanced single-cell RNA sequencing.
To assess the performance, cell capture efficiency, and cross-contamination levels of the new platform.
To apply the platform for analyzing gene expression heterogeneity in patient-derived glioma neurospheres.

Main Methods:

Development of an automated microwell array system for single-cell isolation.
Demonstration of high cell capture efficiency (>50%) and compatibility with barcoded mRNA capture beads.
Evaluation of cross-contamination using fluorescent cell lysate and a human-mouse mixed species scRNA-Seq experiment.
Application of the platform to profile gene expression in glioma neurospheres.

Main Results:

The automated microwell platform demonstrated significantly improved performance over previous implementations.
High cell capture efficiencies and compatibility with commercial barcoding methods were achieved.
Cross-contamination was rigorously evaluated and found to be minimal.
Analysis of glioma neurospheres revealed distinct subpopulations with heterogeneous gene expression.

Conclusions:

The developed automated microwell array platform provides a robust and efficient tool for high-throughput single-cell RNA sequencing.
The system effectively characterizes cellular heterogeneity, offering insights into complex biological systems like glioma.
This technology advances the potential for unbiased expression profiling in diverse biological samples.