Microarrays are tools used to analyze gene expression. They consist of small glass slides containing samples of many genes arranged in a regular pattern. The genes are used to detect mRNA species present in a cell or tissue at a given time, allowing analysis of which genes are actively being expressed. Major uses of microarrays include analysis of gene expression, single nucleotide polymorphisms, and identification of pathogens or tumors. They provide a way to detect differences in gene expression across large numbers of genes in different cell populations on a genome-wide scale.

1. Microarray Technology

2. What Is A Microarray?
“A microarray is a tool for analyzing
gene expression that consists of a
small membrane or glass slide
containing samples of many genes
arranged in a regular pattern.”

3. Uses
• Analysis of gene expression
• SNP analysis
• MHC typing
• Identification of pathogens
• Identification of tumours

4. MICROARRAYS
• The underlying principle of microarray technology is the ability of
DNA to bind to itself and to RNA.
• Analyzing gene expression involves the detection of mRNA species
(transcriptome) present in a cell or tissue at a particular point in time.

5. Microarrays
RNA RNA
Cy3 labelled
cDNA
Cy5 labelled
cDNA
Hybridization

6. Evolution of Microarrays
• One gene / one experiment
– RT-PCR, northern blots, RNase assays
• Macroarrays
– Nylon membranes
– 32P labelled samples
• Microarrays
– Glass slides
– Fluorescent labelled samples
• Affymetrix

7. • There are 3 main types of microarrays
• Glass cDNA microarrays
• Glass oligonucleotide microarrays
• Affymetrix

8. Glass Microarrays
• cDNA arrays
– >1000 nucleotides in length
– cDNA libraries
• Oligonucleotide arrays
– 70-80 nucleotides in length
– Increased specificity

9. Affymetrix
• 25 nucleotides in length
• Mismatch pair
– Single mismatch at centre of probe
– Used to detect & eliminate false results
• 11 probe pairs per gene
• Photolithography

10. Bovine Microarrays
Microarray Format Source of Material
BOTL cDNA Bovine total leukocyte cDNA library & immune
gene amplicons
Pyxis CattleArray 7600 cDNA Bovine spleen & placental cDNA libraries
NBFGC cDNA MARC & BARC cDNA libraries
BMAM cDNA MARC & BARC cDNA libraries
Mammary gland specific
Endometrial/placental
microarray
cDNA Bovine placental & endometrial cDNA libraries
Bovine immune-endocrine
microarray
cDNA Bovine immune & endocrine gene amplicons
Bovine MHC class I
microarray
oligos BoLA DRB3 & DQA sequences
BoMP microarray
RIGUA
cDNA
Oligos
Bovine macrophage cDNA library
Bovine immune & inflammatory gene amplicons
Affymetrix oligos Various cDNA libraries
ARK-Genomics cDNA Various cDNA libraries

11. DNA MICROARRAYS CAN BE
USED TO DETECT DIFFERENCES
IN THE LEVELS GENE
EXPRESSION IN DIFFERENT
POPULATIONS OF CELLS ON A
GENOME-WIDE LEVEL.

12. GENE EXPRESSION = A GENE’S
ABILITY TO MAKE A GENE
PRODUCT.
MOST GENES CODE FOR
PROTEINS (PROTEIN ENCODING
GENES) THAT WHEN EXPRESSED,
PRODUCE A GENE-SPECIFIC
PROTEIN.

13. DNA MICROARRAYS
• A small 1 square centimeter chip that’s divided into thousands
of squares.
• Each square contains many copies of a single gene.
• Originally developed by Patrick Brown at the Stanford
University School of Medicine to determine which genes are
involved in yeast cell sporulation.

14. APPLICATIONS OF DNA
MICROARRAY ANALYSIS.
• Genes that are involved in the development of an organism.
• Genes that are activated as a family of genes (gene expression
profiling).
• Genes that are involved in human cancers.
• Earlier diagnosis of human cancers.

15. EXAMPLE OF A CANCER SUBTYPE
DETERMINED VIA DNA
MICROARRAY ANALYSIS.
• Two subtypes of diffuse large B cell lymphoma.
• One group of tumor cells expressed a large group of genes that
are involved in early B cell development.
• Another group of tumor cells expressed a large group of genes
that are involved in late B cell development.

16. Microarrays have many uses.
1. Major use is to investigate gene expression.
2. mRNA isolated from a cell gives a snap-shot of
the events occurring at that time.