Gene expression analysis

Overview

Gene expression is the conversion of heritable, genetic information into RNA or protein. Studying differences and changes in gene expression are important measures for understanding biological systems, including normal development and disease progression.

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What is gene expression analysis?

Gene expression is the process of using information encoded in genes to synthesize a functional gene product. Since genes are transcribed into RNA, which is either translated into protein or serves as a functional RNA end product [e.g., non-coding RNAs (ncRNAs) and long, non-coding RNAs (lncRNAs)], RNA transcript levels are generally equated to a measure of expression of the gene. Thus, gene expression analysis typically quantifies either messenger RNA (mRNA) levels as the first step towards protein expression, or quantifies non-translated, functional RNA.

Why measure gene expression?

Linking the expression of specific genes to a biological process or phenotype helps scientists understand gene function, biological pathways, and the genes that regulate development, cell behavior, cell signaling, and disease. The specific gene expression patterns or “gene signatures” associated with a biological state can serve as biomarkers for that condition, and, in the example of disease, can be used in identification, diagnosis, and assessment of treatment success. Similarly, determining changes in gene activity resulting from specific environmental and physical factors can reveal the effect of these factors. Such evaluation helps medical professionals understand the impact of medications and facilitates research towards developing more effective drugs. Likewise, this analysis can identify conditions under which specific crops are induced to thrive.

How is gene expression measured?

Measuring gene expression has traditionally involved isolating an intact RNA fraction from samples, immobilizing it, and detecting and quantifying the RNA transcripts of interest. This is usually done using a transcript-specific, labeled probe. Gene expression techniques that use this approach have been limited by their ability to study only a few transcripts per experiment. These include: northern blotting, dot blotting, ribonuclease protection assays (RPAs), serial analysis of gene expression (SAGE), and differential or subtractive hybridization.

Current approaches provide greater detection efficiency and allow for increased target and sample number. They usually involve adding multiple probes to an RNA fraction or directly to a cell lysate. These include quantitative PCR (qPCR), digital PCR (dPCR), next generation sequencing (NGS), microarrays and panels, and in situ hybridization, including fluorescent in situ hybridization (FISH).

Get started with gene expression using qPCR

One of the most widely used methods for analyzing gene expression is qPCR, also called real-time PCR. qPCR is performed following cDNA synthesis. It uses an assay, comprised of a primer pair with a fluorescent reporter molecule (probe) or intercalating dye, to measure amplification of the target sequence during PCR temperature cycling.

IDT offers a selection of qPCR reagents to assess gene expression. Order ready-to-use PrimeTime qPCR Assays or design a custom assay. Both probe-based and intercalating-dye based assay options are available.

PrimeTime qPCR Probe and Primer Assays

PrimeTime qPCR Probe Assays are 5′ nuclease assays that include a library of predesigned assays for human, mouse, and rat sequences. Custom assays may be created for these or other species using the PrimerQuest Tool. Predesigned and custom assays are available in tubes or plates.

PrimeTime qPCR Primer Assays for use with intercalating dyes, such as SYBR® Green dyes, include predesigned assays for human, mouse, or rat sequences. Custom assays may be created for these and other species using the PrimerQuest Tool. Predesigned and custom assays are available in tubes or plates.

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