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DNA Microarray Technique (DNA Chip)

What genes are expressed by a specific cell? That is one of the questions which DNA microarrays or DNA chips can answer. The results may look something like this? But how do we even interpret this DNA chip? What follows, is an example of how to carry out this DNA microarray technique AND how to interpret it: First, RNA is extracted from two samples, and is transcribed into cDNA using reverse transcriptase and during this step, each cDNA molecule is fluorescently labeled with different colors. In our case, sample 1 has a red label and sample 2 has a yellow label. Now, let us examine the microarray closer. We can see that it contains many individual spots, and when we zoom in further we can see that each spot is coated with multiple short, identical, oligonucleotide probes of a specific gene. By observing which of our sample cDNAs bind to which spot we know which gene is expressed in which sample. Depending on which gene is present either none, one or both of our sample cDNAs may bind to the oligonucleotide of the gene present on the spot. So in our hypothetical case, if a specific spot is red, it means that the gene of that particular spot is expressed in sample 1 but not in sample 2. If it’s yellow, the gene is expressed in sample 2 but not 1 and if it’s orange it is expressed in BOTH 1 and 2. This whole plate is prepared and analyzed in one step and the final result may look something like this! A laser and a detector are used together to excite and detect the re-emitted light from the fluorescently labeled cDNA. If you would like to know more about how the cDNA used for this technique is created, check out this video! UNTIL NEXT TIME!