Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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 microarray-based...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A cytoplasmic index for quantifying immune-related A-to-I RNA editing.

Genome biology·2026

Same author

A transcriptome-wide systematic search does not detect A-to-I RNA editing in <i>cis</i>-antisense RNA duplexes.

Genome research·2026

Same author

Off-target RNA editing hotspots caused by base editors.

Molecular therapy : the journal of the American Society of Gene Therapy·2025

Same author

Landscape of A-I RNA editing in mouse, pig, macaque, and human brains.

Nucleic acids research·2025

Same author

A systematic evaluation of the therapeutic potential of endogenous-ADAR editors in cancer prevention and treatment.

NAR cancer·2025

Same author

Global quantification of off-target activity by base editors.

Methods in enzymology·2025

Search research articles

Related Experiment Video

Updated: May 31, 2026

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Barcoding bias in high-throughput multiplex sequencing of miRNA.

Shahar Alon¹, Francois Vigneault, Seda Eminaga

¹Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.

Genome Research

|July 14, 2011

Summary

DNA barcodes used in multiplexed miRNA sequencing introduce significant bias. Adding barcodes during PCR amplification, not adapter ligation, eliminates this bias, improving miRNA expression accuracy.

More Related Videos

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

Published on: August 3, 2011

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Published on: November 18, 2014

Related Experiment Videos

Last Updated: May 31, 2026

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

Published on: August 3, 2011

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Published on: November 18, 2014

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Second-generation sequencing is the preferred method for miRNA detection and expression profiling.
Multiplexing multiple samples in a single sequencing run is desirable for efficiency.
This requires DNA barcodes to identify individual miRNA libraries.

Purpose of the Study:

To investigate the impact of DNA barcodes on miRNA expression profiles in multiplexed sequencing.
To identify methods for mitigating barcode-induced bias in miRNA expression analysis.

Main Methods:

Comparison of miRNA expression profiles generated using barcodes introduced via adapter ligation versus PCR amplification.
Quantification of bias relative to expected Poisson noise.

Main Results:

Adapter ligation of DNA barcodes introduces significant bias in miRNA expression profiles, masking true differences.
This bias exceeds expected random noise (Poisson noise).
Introducing barcodes during PCR amplification effectively eliminates this bias.

Conclusions:

The method of DNA barcode introduction critically affects miRNA expression profiling accuracy.
PCR-based barcoding is essential for accurate, unbiased miRNA expression measurements in multiplexed sequencing experiments.
The accuracy of multiplexed miRNA expression profiling is dependent on the number of samples analyzed.