Basic introduction of DNA microarray

1. DNA
Microarray:
Sunil Bhandari
Balkumari College
©sunilbhandariv@gmail.com

2. Microarray
Microarrays are used in various areas such as:
• Functional genomics research (retrieving differentially expressed genes)
• Target discovery (organism identification, gene identification)
• Biomarker determination
• Pharmacology
• Toxicology (to find effects of drugs and toxic compounds respectively on
living cells)
• Predicting disease prognosis, and
• sub classifying disease
Microarrays are glass slides that contain
particular molecules (DNA-probes) attached to their
surface by robotic arms, each of which can
specifically bind (hybridize) a particular target
molecule on our sample.
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3. In general, DNA microarrays are
microscope slides that are printed
with thousands of tiny spots in
defined positions, with each spot
containing a known DNA sequence
or gene called Probe.
Average size of array in slide =1.28cm X
1.28cm = 1.6384cm2
Average size of each tiny spots =
0.005cm X 0.005cm = 0.000025cm2
Thus average number of spots in
microarray = 1.6384/0.000025 = 65,536
(such tiny spots may ranges from 65 thousand to
6.5 millions per array)
• The probes are designed with average
of 25base pairs long. ©sunilbhandariv@gmail.com

4. Types of microarrays
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5. Process of microarray:
Sample
mRNA isolation
cDNA preparation
cDNA labelling
Mixing-hybridization
Washing Scan the array Array image
Image processing
Intensity data retrieval
Data expression
Fig: Process of Microarray
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6. Process of microarray:
1. mRNA molecules are typically isolated from both an
experimental sample and a reference sample. (For example, the reference
sample could be collected from a healthy individual, and the experimental sample could be
collected from an individual with a disease like cancer.)
2. The two mRNA samples are then converted into
complementary DNA (cDNA), and each sample is labeled with a
fluorescent probe of a different color. (The experimental cdna sample may
be labeled with a red fluorescent dye, whereas the reference cdna may be labeled with a
green fluorescent dye.)
3. The two samples are then mixed together and allowed to
bind to the microarray slide. The process in which the cDNA
molecules bind to the DNA probes on the slide is called
hybridization.
4. Following hybridization, the microarray is scanned to measure
the expression of each gene hybridized on the slide.
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7. 5. If the expression of a particular gene is higher in the experimental
sample than in the reference sample, then the corresponding spot
on the microarray appears red. In contrast, if the expression in the
experimental sample is lower than in the reference sample, then
the spot appears green.
7. Finally, if there
is equal
expression in the
two samples, then
the spot appears
yellow.
The data gathered through microarrays can be used to create gene
expression profiles, which show simultaneous changes in the expression of
many genes in response to a particular condition or treatment.
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8. Processing of image spots
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9. Expression of microarray data
1. Ratio data
Ratio data is calculated for comparison of two or more sample
based on the amount their fluorescence intensity produced on
specific spots. Different color dye (Cy-3 and Cy-5) are used to label
the individual sample and respective color produced after
illumination is captured. These data gives the individual as well as
relative information of the sample under study,
2. Intensity data
Intensity data represents the microarray outcomes of individual
data of single type of sample labelled with single type of dyes. Color
intensity of fluorescence gives the information about identification
of sample as well as strength/amount of targets in sample. Data are
not meant for comparison purpose.
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10. Application of Microarray
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