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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 microarray-based...

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Related Experiment Video

Updated: May 26, 2026

Laser-capture Microdissection of Human Prostatic Epithelium for RNA Analysis

Laser-capture Microdissection of Human Prostatic Epithelium for RNA Analysis

Published on: November 26, 2015

Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing.

Sam E V Linsen¹, Edwin Cuppen

¹Hubrecht Institute, Utrecht, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|December 7, 2011

Summary

This summary is machine-generated.

This study compares three small RNA sequencing library preparation protocols for digital gene expression profiling. Each method offers unique trade-offs in terms of cost, multiplexing capability, and bias for microRNA detection.

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Last Updated: May 26, 2026

Laser-capture Microdissection of Human Prostatic Epithelium for RNA Analysis

Laser-capture Microdissection of Human Prostatic Epithelium for RNA Analysis

Published on: November 26, 2015

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Digital gene expression (DGE) profiling is crucial for analyzing small RNA species, including microRNAs.
Small RNA library preparation typically involves adapter ligation, reverse transcription, and PCR amplification.

Purpose of the Study:

To describe and compare three distinct protocols for generating small RNA sequencing libraries for SOLiD(TM) platform.
To evaluate the advantages and disadvantages of each protocol regarding multiplexing, cost-efficiency, bias, and precision.

Main Methods:

Adaptation of the Ambion SREK(TM) protocol for multiplexing.
Utilization of a modified protocol based on modban for cost-efficiency.
Implementation of a poly(A)-based protocol for reduced bias.

Main Results:

The Ambion SREK(TM)-adopted protocol facilitates sample multiplexing.
The modban-based protocol is cost-effective but exhibits bias towards specific microRNAs.
The poly(A)-based protocol shows less bias but reduced precision due to A-tailing.

Conclusions:

Each small RNA library preparation protocol presents a unique balance of benefits and drawbacks.
Protocol selection depends on specific experimental needs, considering factors like barcode inclusion, cost, and desired accuracy for microRNA analysis.