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Related Experiment Video

Updated: May 15, 2026

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Multiplex Illumina sequencing using DNA barcoding.

Koon Ho Wong¹, Yi Jin, Zarmik Moqtaderi

¹Harvard Medical School, Boston, Massachusetts, USA.

Current Protocols in Molecular Biology

|January 5, 2013

Summary

Multiplex sequencing uses DNA barcodes to pool and sequence multiple samples, saving costs and time. This protocol efficiently prepares up to 96 ChIP samples for Illumina sequencing, applicable to other applications.

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Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Published on: June 3, 2019

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Modern sequencing generates vast amounts of data, often exceeding experimental needs, particularly for small genomes.
Multiplex sequencing, using DNA barcodes to tag and pool samples, offers an economical and efficient solution.
Bioinformatic analysis requires subsequent sorting of pooled sequence data by barcode.

Purpose of the Study:

To present a barcoding protocol for preparing up to 96 ChIP samples for multiplex sequencing.
To enable simultaneous sequencing of multiple samples in a single Illumina flow cell lane.
To provide a strategy adaptable for larger sample numbers and diverse sequencing applications.

Main Methods:

Development of a barcoding protocol for sample preparation.
Utilizing short, unique DNA sequences (barcodes) for sample identification.
Pooling barcoded samples for simultaneous sequencing on the Illumina platform.

Main Results:

Successful preparation of up to 96 ChIP samples for multiplex sequencing.
Demonstration of a cost-effective and efficient method for deep sequencing.
The protocol is designed for the Illumina platform but is generalizable.

Conclusions:

The presented barcoding protocol facilitates efficient multiplex sequencing of ChIP samples.
This strategy significantly reduces costs and increases efficiency in genomic experiments.
The method is versatile and can be applied to various sequencing applications and platforms.