http://www.biomed.miami.edu/arrays/images/agilent_array.jpg

1
Example of a DNA array used to studygene
expression (note green, yellow red colors also
note that only part of the totalarray is
depicted)
http//www.biomed.miami.edu/arrays/images/agilent_
array.jpg
2
DNA Arrays Two Purposes

1. Genotype individuals on polymorphisms(read text
   for example).
2. Study gene expression (these slides).

3
MethodsStudying Gene Expression
Step 1 Create a DNA array (gene chip) by
placing single-stranded DNA for each gene to be
assayed into a separate well on the chip.
4
DNA Array Single-stranded copy DNA foreach gene
in a different well.
5
MethodsStudying Gene Expression
Step 2 Extract mRNA from biological tissues
subjected to an experimental treatment and from
the same tissue subjected to a control treatment.
Step 3 Make single-stranded DNA from the mRNA
using color coded nucleotides.
6
Extract mRNA from Control Cells
Extract mRNA from Experimental Cells
Make single-stranded cDNA using green nucleotides
Make single-stranded cDNA using red nucleotides
cDNA complementary DNA (DNA synthesized from
RNA)
7
MethodsStudying Gene Expression
Step 4 After making many DNA copies of the RNA,
extract an equal amount of cDNA from the controls
experimentals and place it into a separate
container.
8
(No Transcript)
9
MethodsStudying Gene Expression
Step 5 Extract a smallamount in a pipette.
10
Methods
Step 6 Insert into first well.
11
Methods
insert intosecond well, etc.
Step 7 Extractmore cDNA and
12
Methods
Step 8ff Continue until all wells arefilled.
13
Methods
Step 9 Allow to hybridize, then wash away all
single-stranded DNA.
14
Result

1. Some wells have no color-coded cDNA (no mRNA in
   either type of cell)
2. Some wells have only red (i.e., expressed only in
   experimental cells)
3. Some wells have only green (i.e., expressed only
   in control cells)
4. Some wells have both red and green in various
   mixtures (expressedin both experimental and
   control cells)

15
Methods
Step 10 Scan with a laser set to detect the
color process results on computer.
16
Results
The colors denote the degree of expression in the
experimental versus the control cells.
Gene not expressed in control or in experimental
cells