DNA microarray flow chart and
predictions
Mrs. Stewart
Medical Interventions
Central Magnet School

How does a DNA Microarray illustrate the
differences in gene expression between two
tissue samples?

DNA Microarray Video

Create a flowchart for the steps in a DNA
Microarray in your lab journals
Print singlestranded DNA
gene sequences
onto a microarray
(slide)
Isolate mRNA
from normal and
“experimental”
cells
Prepare
flourescent
(labeled) cDNA
from each of the
mRNA samples
Hybridize
(place labeled cDNA
sequences onto printed
slides with known
genes – complementary
sequences will bind)
Visualize
results
Analyze

Grandpa Joe, Judy Smith’s father, has been a
smoker for the past thirty years. Last year,
Grandpa Joe came down with a cold that
turned into pneumonia. It took him more than
a month to recover. The family is very
concerned he is going to develop lung cancer.
They heard about a study being conducted at
the local hospital that is exploring lung-cancer
associated genes in smokers and non-smokers.
The family convinces Grandpa Joe to
participate in the study in order to learn more
about his risk for developing lung cancer.

The study is investigating six genes thought to
be involved with lung cancer using DNA
microarray technology. The researchers hope to
compare gene expression of the six genes of
interest between smokers and non-smokers in
order to gain more knowledge of what causes a
normal lung cell to become cancerous. You
have been assigned to the study. Your first task
is to learn more about the six genes of interest.
Gene 1:
Human carcinoembryonic
antigen (CEACAM6)
This gene codes for a
protein that is located in
the extracellular matrix.
This protein is involved
with adhesion between
cells and is thought to be
a proto-oncogene and
when over-expressed is
an oncogene.
Gene 2:
Surfactant protein B
(SFTPB)
This gene codes for an
extracellular protein. This
protein enhances the rate of
spreading and increases the
stability of pulmonary
surfactant, a lipid-rich
material that prevents lung
collapse by lowering surface
tension at the air-liquid
interface in the alveoli of the
lungs.
Gene 3:
P53 tumor suppressor
(TP53)
Gene 4:
SRY
This gene codes for a
protein that is located in
the mitochondria and in
the nucleolus. This
protein is involved with
cell cycle checkpoints.
This gene is a tumor
suppressor gene and is
thought to be the
“Guardian of the
Genome.”
This gene codes for a
protein that is located in the
nucleus. The protein that
this gene codes for is testisdetermining factor (TDF)
which initiates male sex
determination. This protein
has no function in lung cells.
Gene 5:
Cytochrome P450
(CYP1A1)
This gene codes for a
protein that is located in
the endoplasmic reticulum.
The protein catalyzes
reactions involved in drug
metabolism and
synthesizes cholesterol,
steroids, and other lipids.
The expression of this
protein is induced by some
polycyclic aromatic
hydrocarbons (PAHs),
some of which are found in
cigarette smoke.
Gene 6:
Glypican 3(GPC3)
This gene codes for a protein
that is located in the plasma
membrane and extracellular
matrix. The gene controls
cellular response to damage
and may control cellular
growth regulation and
apoptosis. This gene is
considered to be a tumor
suppressor gene for lung
cancer.



Place one drop from each gene onto the
correspondingly numbered spot on the
microarray slide
These will harden in one minute
These spots represent the single-stranded DNA
from each of the genes

Obtain a cDNA dropper bottle (Hybridization
Buffer) and place one drop onto each of the
numbered spots on the microarray slide


Careful!! Do not touch the tip of the bottle to the DNA
spots
The cDNA dropper bottle contains a solution of
labeled cDNA from Grandpa Joe’s lung cells
and a non-smoker’s lung cells mixed together


Place your DNA microarray slide onto a white
piece of paper to observe results.
After you complete your student response
sheet: Wipe off the six spots on your slide with
a paper towel. Wash and dry your slide.


Draw a diagram of the slide in your laboratory
journal. Make sure to clearly indicate which
gene is on which spot.
Draw your results on the Student Response
Sheet. Include a description of the color of each
spot. Analyze the results.
Human carcinoembryonic antigen (CEACAM6)
Surfactant protein B (SFTPB)
P53 tumor suppressor (TP53)
SRY
Cytochrome P450 (CYP1A1)
Glypican 3(GPC3)
This gene codes for a protein that is located in the extracellular
matrix. This protein is involved with adhesion between cells and
is thought to be a proto-oncogene and when over-expressed is an
oncogene.
This gene codes for an extracellular protein. This protein enhances the
rate of spreading and increases the stability of pulmonary surfactant, a
lipid-rich material that prevents lung collapse by lowering surface
tension at the air-liquid interface in the alveoli of the lungs.
This gene codes for a protein that is located in the mitochondria and in
the nucleolus. This protein is involved with cell cycle checkpoints. This
gene is a tumor suppressor gene and is thought to be the “Guardian of
the Genome.”
This gene codes for a protein that is located in the nucleus. The protein
that this gene codes for is testis-determining factor (TDF) which
initiates male sex determination. This protein has no function in lung
cells.
This gene codes for a protein that is located in the endoplasmic
reticulum. The protein catalyzes reactions involved in drug metabolism
and synthesizes cholesterol, steroids, and other lipids. The expression
of this protein is induced by some polycyclic aromatic hydrocarbons
(PAHs), some of which are found in cigarette smoke.
This gene codes for a protein that is located in the plasma membrane
and extracellular matrix. The gene controls cellular response to
damage and may control cellular growth regulation and apoptosis. This
gene is considered to be a tumor suppressor gene for lung cancer.




Pink result = Gene transcription (expression) is
induced
Blue result = Gene transcription (expression) is
suppressed
Purple result = Gene transcription (expression) is
not affected
Clear/white result = Gene not expressed
**These colors differ from a regular DNA microarray in
which Red, Yellow and Green are used.




When the ratio is greater than one, the gene is induced by
tumor formation. This means that the gene transcription
was more active in cancer cells than in normal cells.
When the ratio is less than one, the gene is suppressed by
tumor formation. This means that the gene transcription
was less active in cancer cells than in normal cells.
When the ratio is equal to one, the gene is not affected by
tumor formation. This means that the gene transcription
was the same in cancer cells as it was in normal cells.
When the ratio is zero, the gene is not expressed in either
cell.

How does a DNA Microarray illustrate the
differences in gene expression between two
tissue samples?