Advanced Topics in Biology Name: ______________________Date: _______________Block: _____
LAB: Microarray UNIT: Gene Regulation
Microarray Lab
Data and Analysis
Take a photo of your final card and submit it and record your results in Table 1 with the colors red, green,
yellow or black.
Table 1. Results of microarray
1 2 3 4 5 6 7 8
Normal Up Down Blank Gene 1 Gene 2 Gene 3 Gene 4
Patient 1 Yellow red Green X X Yellow Green Red
Patient 2 Yellow red Green X Green Red Green Red
Patient 3 Yellow red Green X Green Yellow Green X
Patient 4 Yellow red Green X Green Yellow Green Red
Questions
1. How are the individual spots on a microarray chip identified and analyzed? What does a red, green,
yellow or black (no fluorescence) spot represent?
The individual spots on the microarray chip contain specific DNA probes that represent the
differing genes. They are identified and analyzed with a laser, which excites the fluorescent
dyes which represent if the cDNA molecules have found their corresponding probe on the
chip. If the gene is downregulated in cancer cells, then it would fluoresce green. If the gene is
upregulated in the cancer cells, then it would fluoresce green. If the gene is expressed equally
in both types of cells, then it will fluoresce yellow. The black spots, which do not fluoresce,
mean that there is no matching probe on the chip and therefore are not expressed in either
cell type.
2. Interpret your results. Which genes were upregulated or downregulated in the cancer
cells? What are some likely candidate genes for genes 1 through 4?
Gene 4 mostly fluoresced red, therefore it is probably upregulated for cancer cells and is
likely an oncogene. Gene 3 and Gene 1 were fluorescent green for every patient therefore, it
is downregulated in cancer cells and is probably a type of cell like a tumor suppressor gene.
Adapted from [Link]
Advanced Topics in Biology Name: ______________________Date: _______________Block: _____
LAB: Microarray UNIT: Gene Regulation
normal cell. Gene 2 fluoresces yellow, so this signifies it has similar abundance in both cancer
and normal cells, therefore it is probably a type of cell not affected by cancerous processes in
the body like taste receptors or reproduction.
3. What is the core technology behind microarrays and why it is important for biotechnology
and medicine.
The core concept behind the microarrays is DNA hybridization. This process first needs the
production of complementary base-pairing to create single stranded cDNA from the patient
samples. This cDNA is washed over the chip. If the sample in fact has a matching gene, it will
hydrize to the complementary DNA probe and be anchored to the slide. This process is
important as it allows scientists to screen the expression of thousands of genes
simultaneously, which can lead to many applications like the 23 & Me non profit, where they
investigate the origins of genes from the samples of their consumers.
4. How are cDNAs libraries made?
cDNAs libraries are made by extracting RNa from cells, using enzyme Reverse Transcriptase
to create complementary DNA copies. A second strand is created by synthesizing a double
stranded DNA version which can be inserted into plasmids and cloned in bacteria. This
process creates a collection of DNA that represents the active genes of those cells at a specific
time. Using mRNA as a template, allows for a process which can omit the introns, so the
resulting DNA library shows only the protein-coding sequences (the exons).
5. What information have DNA microarrays made possible?
The technology of microarrays has led to the possibility of checking thousands of genes at one time.
Specifically, it allows for Gene Expression profiling. This has allowed researchers to classify cancers into
specific subtypes, not based on viable appearances, leading to personalized medicine, where treatment
can be tailored to these specific genetic mutations of patients. An application of personalized medicine
can even be through the company 23 & Me, as the company through the customer’s salvia sample can
scan for hundreds of thousands of specific single-nucleotide polymorphisms. This genotyping process can
identify genetic markers linked to medical history.
Adapted from [Link]