Name __________________
Class Period __________
Group _________________
Gene Expression—Microarrays in Action
Introduction:
Nearly all the cells in our body have the same DNA. How is it, then, that our cells can look and
function so differently? The trick is in each cell’s ability to change how much each gene makes.
For example, we’ve learned about pigment cells called melanocytes and that they are responsible
for the color of skin, eyes, and hair (among other things). One thing that makes the melanocytes
special is that they produce, or “express” more of the gene for the pigment melanin than other
cells (and melanin is the pigment that changes our skin, eye, and hair color).
DNA (gene)

In Cells
mRNA 
Protein (melanin)
Cells in our body can also react to things in the environment to change how they behave. For
example, if you were to go to high altitude, your muscles will feel tired more quickly because there
is less oxygen in the air, less oxygen in your blood, and less oxygen getting to your muscles at high
elevations. Cells in your kidneys respond lower amounts of oxygen in your blood by expressing
more mRNA for the gene EPO. EPO makes a hormone that increases the number of red blood cells
in your blood, and those extra red blood cells make it so that you can carry more oxygen in your
blood to your tired muscles!
Sometimes scientists think that there will be changes in the amount of RNA genes produce in some
tissue, but they don’t know exactly what to look for. When that happens, they use a technology
called an RNA microarray. Microarrays measure how much RNA is produced from a gene, but for
thousands of different genes at a time. Microarrays use fluorescent dyes to compare the amount
that genes produce between two different samples (for example, comparing the amount of EPO in
people at sea level and people who live in the mountains) and tell you if the amount has gone up,
down, or hasn’t changed.
DNA (gene)
For a Microarray

mRNA 
Fluorescent cDNA
Today we will simulate a microarray experiment and see what whether the amount that some
genes “express” in our samples is different.
Your Task:
s
Protocol
1)
We will pass out a microarray “plate” to your group. Record the plate number on your
data sheet (VERY IMPORTANT).
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2)
Name __________________
Class Period __________
Group _________________
The microarray compares normal tissue and our mystery cDNA, we have already mixed
normal cDNA with the mystery cDNA. Go get a sample of cDNA and take it to your table.
Record your mystery cDNA Sample ID (A or B) on your data sheet—VERY
IMPORTANT.
3)
It is important to know which way to “read” your microarray plate. Position your plate so
that the A1 square is in the upper left (see the diagram on the data sheet).
3)
Add three drops of your mystery cDNA to each well of the microarray plate. Record the
color of each well of the plate on your data sheet (use colored pencil or just write the
color).
4)
Look at your microarray gene key to determine which genes are producing more mRNA
(and cDNA) in your mystery samples:

More mRNA / cDNA in mystery sample = Pink / Red

Less mRNA / cDNA in mystery sample = Green

No change = Blue / Purple
Data Sheet
Microarray Plate ID: _______________________________________
Mystery Sample ID: _______________________________________
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Name __________________
Class Period __________
Group _________________
Microarray Plate
A
1
GRIN2B
2
NR4A2
3
GAPDH
4
OPRK1
5
BDNF
6
ACTB
7
MIF
8
CREB1
B
GABRA1 CARTPT NTRK2
DRD2
MAG
EGFR
SIRT1
TBP
Questions
1)
Exercise is known to increase expression of BDNF, CREB1, and GRIN2B while lowering
GABRA1, MAG, and MIF.
Cocaine use if known to increase expression of BDNF, CARTPT, CREB1, and EGFR1 and
decrease DRD2, OPRK1, and NTRK2.
Which mystery cDNA sample did you get?
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2)
Microarrays compare the amount of RNA/cDNA between two different conditions (for
example normal and cocaine use). What color changes would you expect to see in our
microarray if we compared two similar samples (like two samples from cocaine users)?
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3)
Choose one of the genes that has changed expression in your microarray. Use the class
laptops to look up your gene (using either the NIH’s website:
http://www.ncbi.nlm.nih.gov/gene or Genecards: http://www.genecards.org/, some of the
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Name __________________
Class Period __________
Group _________________
genes even have Wikipedia entries). Write down at least three pieces information about
the gene (for example, BDNF is short for “brain-derived neurotrophic factor!”).
Name of gene: ________________________________________
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