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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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Updated: Jul 7, 2026

Optimizing Tear Collection in Mice for mRNA and Protein Analysis

Optimizing Tear Collection in Mice for mRNA and Protein Analysis

Published on: July 19, 2024

Optimization of minuscule samples for use with cDNA microarrays.

Susan McLean Hunter¹, Fiona C Mansergh, Martin J Evans

¹School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10, 3US, Wales, UK.

Journal of Biochemical and Biophysical Methods

|February 12, 2008

Summary

This study optimized microarray protocols for small samples like embryonic stem cells. The streamlined method enables accurate gene expression profiling from minimal biological material.

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Last Updated: Jul 7, 2026

Optimizing Tear Collection in Mice for mRNA and Protein Analysis

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Published on: July 19, 2024

Performing Custom MicroRNA Microarray Experiments

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Published on: October 28, 2011

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Microarray technology enables high-throughput gene expression profiling.
Analyzing small biological samples presents unique technical challenges.
Optimized protocols are crucial for reliable gene expression analysis.

Purpose of the Study:

To develop and validate a streamlined microarray protocol for small samples.
To identify optimal methods for RNA preparation, amplification, labeling, and array analysis.
To enable accurate transcriptome mapping of limited biological materials.

Main Methods:

Comparison of various RNA extraction kits (Mini RNA Isolation kit).
Evaluation of RNA amplification methods (RiboAmp kit).
Assessment of indirect labeling techniques (Atlas PowerScript Fluorescent Labelling kit).
Analysis of array data using Limma package with print tip Loess normalization and "normexp" function.
Reverse transcription polymerase chain reaction (RT-PCR) for validation.

Main Results:

An optimal protocol was established using specific kits for RNA extraction, amplification, and labeling.
The Limma package with print tip Loess normalization and specific background adjustment proved most effective.
Reverse transcription polymerase chain reaction (RT-PCR) confirmed array results without amplification bias.

Conclusions:

The developed protocol is highly effective for gene expression profiling of small samples, including early-stage mouse embryos and embryonic stem cells.
This method facilitates accurate transcriptome mapping of limited biological samples.
The protocol addresses challenges associated with analyzing minute amounts of biological material for gene expression studies.