Microarrays: Tools

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MicroarraysTools Interpretation of Data
Kirsty Jensen
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Microarrays

• What is a microarray?
• How the technology has evolved
• Macroarrays
• Glass microarrays
• Affymetrix
• Designing a microarray experiment
• Choice of arrays
• Experimental design
• RNA samples
• Analysis
• Scanning
• Quantification of spots
• Normalization
• Statistical analysis
• Identification of genes of interest
• Validation

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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.
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Uses

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

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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.

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Evolution of Microarrays

• One gene / one experiment
• Northern blots, RNase assays, RT-PCR
• Hypothesis driven
• Macroarrays
• Nylon membranes
• 32P labelled probes

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Macroarrays
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Evolution of Microarrays

• One gene / one experiment
• RT-PCR, northern blots, RNase assays
• Hypothesis driven
• Macroarrays
• Nylon membranes
• 32P labelled samples
• Microarrays
• Glass slides
• Fluorescent labelled samples
• Two samples per microarray

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Microarrays
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Glass Microarrays

• cDNA arrays
• gt1000 nucleotides in length
• cDNA libraries
• Oligonucleotide arrays
• 70-80 nucleotides in length
• Increased specificity

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Evolution of Microarrays

• One gene / one experiment
• RT-PCR, northern blots, RNase assays
• Hypothesis driven
• Macroarrays
• Nylon membranes
• 32P labelled samples
• Microarrays
• Glass slides
• Fluorescent labelled samples
• Affymetrix

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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

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Affymetrix - Construction
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Affymetrix
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Affymetrix
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Bovine Microarrays
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Conclusions (1)

• Microarrays have many uses.
• Major use is to investigate gene expression.
• mRNA isolated from a cell gives a snap-shot of
  the events occurring at that time.
• There are 3 main types of microarrays
• Glass cDNA microarrays
• Glass oligonucleotide microarrays
• Affymetrix