microRNA Microarray Service - Technical Bulletin

Dual Sample vs Single Sample Experiments

Dual Sample

A dual-sample assay is used when two samples are compared with each other. The assay does not involve chip-to-chip variations and therefore may reveal very small differences between the two samples. The assay is especially suitable when paired samples are studied, such as diseased tissue being compared with an adjacent non-diseased tissue. The assay also has an advantage of lower per-sample cost than single sample assay does.  However, design considerations should be given to minimize dye-related bias.

Single Sample

A single-sample assay is used when multiple independent samples are compared with each other. The assay has the advantage of free of dye-related bias although it has a higher per-sample cost.

Minimize Dye Bias in Dual Sample Assays

Dye swap can be used to eliminate false calls due to dye-related bias in dual sample assays. A good design should have half members of each group labeled with Cy3 and the other half labeled with Cy5.

Example 1:

4 samples (A1,A2, B1, and B2) from an experiment of comparing untreated versus treated samples with 2 biological repeats for each sample group.

In this example, samples on each chip do not have to be paired. However, when the samples are paired, “paired T-test” should be used in data analysis.

Example 2:

12 samples from an experiment involving three sample groups of untreated (A1-A4), treated at dosage 1 (B1-B4), and treated at dosage 2 (C1-C4).

Dye Swap Experiment – Two Chips            

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