What are microarrays?
You are part of a research group studying human genes involved in cancer. You have assisted
with the Human Genome Project and have identified genes likely to be involved in cancer. You are
aware of some genes because you found similar sequences in other organisms that have developed
that cancer. You also know the proteins they code for based off of transcribing the sequence and then
translating them. On this basis, you can predict possible functions of the similar human genes you
have identified. However, you find many other sequences with unknown functions.
Your group has decided to use microarrays to compare gene expression in
normal cells vs. abnormal cancerous cells found in humans. Your goal is to
identify the genes that are expressed differently.
Research groups will make “fake DNA” that resembles each unknown gene sequence mentioned above in the first
paragraph. They will then “glue” each sequence in its own well so that when they want to add real genes from normal
cells and cancer cells, they can identify which of the unknown genes are cancerous, genes that are non-cancerous, and
genes that could possibly prevent cancer!
In order for them to identify these genes. Research groups will work with two different tissue samples: one
normal, and one cancerous. First, scientists must extract the mRNA from each sample. A problem with mRNA is that it is
very unstable. Therefore, we need to reverse transcribe the sequences from mRNA back into its complimentary DNA,
known as cDNA.
Answer Questions 1-3
After reverse transcribing the mRNA to cDNA, so that scientist can experiment with it, scientists are able to put
tags on each cDNA called “fluorescent dyes”. The color is what makes real DNA visible to scientists.
Answer Questions 4
In preparation for identifying cancerous genes and non-cancerous genes, the cDNA from the two types of tissue is
labeled with different fluorescent nucleotides. Genes extracted from cancer cells are given a fluorescent red dye.
Genes extracted from healthy cells are given a fluorescent blue dye. All the genes are mixed together so that when
added to the microarray, that each gene will find its way to its specific well.
Answer Questions 5-6
So what does each color on a microarray mean after the real sample cells have been added to each well?
Blue = These spots represent genes that are expressed in the tissue of cells whose cDNA was labeled with the blue dye.
For example, genes from normal lung cells.
Red = These spots represent genes that are expressed in the tissue of cells whose cDNA was labeled with the red dye.
For example, genes from cancerous tumor lung cells.
Purple = The spot is bound to genes in BOTH types of cells. These represent genes that are required by all cells.
White = The spot has no bound cDNA. These represent genes that are not expressed in these cell types.