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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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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

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An exercise to estimate differential gene expression in human cells.

M Ahmad Chaudhry¹

¹Department of Medical Laboratory and Radiation Sciences, Burlington, Vermont 05405; DNA Microarray Facility, University of Vermont, Burlington, Vermont 05405. mchaudhr@uvm.edu.

Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology

|June 4, 2011

Summary

Researchers developed an accessible reverse transcription-polymerase chain reaction (RT-PCR) method to quantify gene expression changes. This technique effectively measures ionizing radiation-induced alterations in human cells for educational and research applications.

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Area of Science:

Molecular Biology
Genetics
Biotechnology

Background:

Gene expression varies across tissue types and is linked to organ function.
Altered gene expression patterns are observed in disease, in response to treatments, infections, and environmental exposures.
Understanding molecular-level disease mechanisms requires studying differential gene expression.

Purpose of the Study:

To develop a simplified, non-radioactive method for examining and quantifying differential gene expression.
To create an educational exercise for college students using reverse transcription-polymerase chain reaction (RT-PCR).
To investigate ionizing radiation-induced changes in human cell gene expression.

Main Methods:

Developed a differential gene expression assay based on RT-PCR.
Isolated total RNA from human cells at various time points post-ionizing radiation exposure.
Converted RNA to cDNA and performed multiplex PCR using gene-specific primers and beta-actin standards.
Quantified gene expression differences using free imaging software.

Main Results:

Successfully established an easy-to-perform, non-radioactive RT-PCR technique for differential gene expression analysis.
Demonstrated the method's ability to detect ionizing radiation-induced gene expression changes in human cells.
Validated the use of beta-actin as an internal standard for accurate quantification.

Conclusions:

The developed RT-PCR method is suitable for educational purposes, enabling students to perform gene expression analysis.
This technique offers a versatile and accessible approach for investigating differential gene expression across various organisms and experimental conditions.
Provides valuable insights into molecular responses to environmental factors like ionizing radiation.