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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...

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Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

Published on: November 10, 2015

DNA microarray-based genome-wide analyses of Plasmodium parasites.

Zbynek Bozdech¹, Sachel Mok, Archna P Gupta

¹School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. zbozdech@ntu.edu.sg

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

|September 20, 2012

Summary

DNA microarrays offer powerful genomic insights into malaria parasites, revealing coordinated gene expression and adaptive responses. Protocols for transcriptional profiling and comparative genomic hybridization are presented for Plasmodium species.

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Area of Science:

Genomics
Molecular Biology
Infectious Diseases

Background:

DNA microarray technology is a rapidly advancing tool for genomic research, particularly in infectious diseases.
Global analyses of Plasmodium parasites using DNA microarrays have significantly advanced our understanding of malaria biology.

Purpose of the Study:

To present protocols for DNA microarray analyses in Plasmodium species.
To enable transcriptional profiling, comparative genomic hybridization (CGH), and ChIP-on-chip analyses.

Main Methods:

Development of protocols for low-density long oligonucleotide DNA microarrays.
Application of methods for RNA purification, DNA amplification, and chromatin immunoprecipitation.

Main Results:

Demonstrated the utility of DNA microarrays for analyzing Plasmodium gene expression and genomic variations.
Characterized Plasmodium transcriptional profiles, sequence polymorphisms, copy number variants (CNV), and chromatin factors.

Conclusions:

The presented protocols are effective for Plasmodium genomic analyses.
Procedures are potentially transferable to other genomic platforms, including next-generation sequencing.