FAQs: MolecuLab 410/420

Q: Could I use a UV Crosslinker to bind the probe DNA to the slide?

While we have not tested this ourselves, there have been good results reported from teachers who have used this technique.

Q: Are there other ways to bake the DNA to the slide?

One alternative is to use a heat block.  When cool, remove the heat block and replace it such that the tube holes are down to provide a flat, contiguous surface.  Turn the heat block on and heat to desired temperature (setting varies by brand).

Another option is to use a hair drier.  Again, we do not tested this ourselves.  One caution is to ensure a firm grip on the slide and take care to not disturb the spots before they are dry.

Q: How hard should my students shake the slides during the wash steps?

We use the general guideline that the students should shake the tubes continuously, but to keep in mind that they have to do 6+ minutes of washing during the post-baking wash and also during the post-hybridization wash.  The wash steps need more than a simple inverting of the tube, but it does not need to be shaken so hard that the students’ arms become fatigued.

Q: We have our microarray images.  How do we interpret the results?

In traditional microarrays different color fluorescent dyes are attached to the target DNAs from different conditions.  Therefore a gene that is expressed in one condition might be green, a gene expressed in another condition might be red and a gene expressed in both conditions might be yellow.  In the case of this simplified microarray, only one fluorescent dye is added.  Therefore one must evaluate the presence of fluorescence on EACH of the grids (representing the different conditions) in order to determine expression of the gene in the different conditions.  The fluorescence could be turquoise, blue, green, yellow, red or a combination of these colors.  Occasionally, one will see a blue or red  “shadow” that covers a large area of the grid.  This is background; it does not affect the fluorescence of the probes and should not be considered when evaluating gene expression.

Q: Where can my students see our microarray results?

Visit the Microarray section to see your microarray results.

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