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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: Apr 12, 2026

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

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics.

Assaf Rotem¹, Oren Ram², Noam Shoresh³

¹Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

|May 23, 2015

Summary

This summary is machine-generated.

High-throughput Single-Cell Labeling (Hi-SCL) in drops enables scalable, cost-effective single-cell RNA sequencing. This novel method indexes individual cells using barcoded oligonucleotides, yielding comparable data to existing techniques but for vastly more cells.

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Last Updated: Apr 12, 2026

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

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Published on: May 23, 2018

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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:

Biotechnology
Genomics
Molecular Biology

Background:

Single-cell data analysis is crucial for understanding cellular heterogeneity.
Existing single-cell technologies often require physical segregation of cells into individual containers.
Scalability and cost remain challenges in high-throughput single-cell analysis.

Purpose of the Study:

To introduce and validate High-throughput Single-Cell Labeling (Hi-SCL) in drops as a scalable method for single-cell RNA sequencing.
To demonstrate the feasibility of using drop-based microfluidics for high-throughput cellular indexing.
To compare the performance of Hi-SCL with existing single-cell RNA sequencing methods.

Main Methods:

Utilizing drop-based microfluidics to encapsulate individual cells.
Employing barcoded oligonucleotides for labeling and indexing of cellular molecules within drops.
Performing cDNA synthesis primed by barcoded oligonucleotides.
Combining barcoded cDNAs for high-throughput sequencing.
Deconvoluting sequencing data using barcodes to obtain single-cell mRNA expression profiles.

Main Results:

Hi-SCL successfully generated single-cell mRNA expression data.
The method demonstrated scalability for assaying a large number of cells.
Data quality and comparability were validated against existing single-cell RNA sequencing techniques.
Proof-of-concept experiments confirmed the method's efficacy.

Conclusions:

High-throughput Single-Cell Labeling (Hi-SCL) in drops offers a scalable and efficient approach for single-cell RNA sequencing.
The technique allows for the analysis of significantly larger cell populations compared to traditional methods.
Hi-SCL holds promise for advancing single-cell genomics research by enabling deeper insights into cellular populations.