DNA Microarrays for Statisticians

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DNA Microarrays for Statisticians

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cDNA Microarray Applications

• Revolutionized gene expression studies
• Diagnose cancer
• Expression profile of tumor progression
• Discriminate types of cancers
• Track time course of gene expression in
  sporulating yeast
• Track cell-cycle genes in synchronized yeast
• Hopefully determine more targets for E2F

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Making a cDNA Microarray
Critical parameters Spot size Spot shape DNA
concentration
Technologies Pins or Needles Pin and Ring Inkjet
Printer
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1..24
Wash
AP
17
384 Well Plates
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(No Transcript)
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Target Generation
RNA
Sense
5
3
AAAAA
DNA
TTTTT
Anti
5
3
Reverse Transcriptase
DNA
Sense
5
3
DNA Polymerase
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A Yeast Microarray
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Affymetrix Photolithography
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(No Transcript)
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Experimental Protocol

• Isolate total RNA from 8-10hr old embryos
• Make cDNA
• Make biotinylated cRNA
• Hybridize 16 hours at 45C
• Wash and stain
• Scan
• Analyze(generate average difference for each
  probe set)

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Target Generation
RNA
Sense
5
3
AAAAA
T7 comp primer
TTTTT
DNA
Anti
5
3
Reverse Transcriptase
DNA
Sense
5
3
DNA Polymerase
RNA
Anti
5
3
RNA polymerase