Dna Chip
An Introduction to DNA microarrays
Rebecca Fry, Ph.D.
http://www.buffalo.edu/UBT/UBT
What is a DNA Microarray? genes or gene fragments attached to a substrate (glass)
Tens of thousands of spots
Hybridized slide
Two dyes
Image analyzed
1
The Beginnings of Microarray Technology
Lockhart et al., 1996
Nature Biotechnology
“Expression monitoring by hybridisation to high-density oligonucleotide arrays” Schena et al., 1995
Science
“Quantitative monitoring of gene expression patterns with a complementary
DNA microarray”
8 years later
4162 references
2
Uses and Applications
Target identification
Pathway mapping
Gene screening
Mechanism of Action Studies
Disease characterization
Molecular Diagnosis of Disease
Personalized medicine
Developmental Biology
Prediction of Drug Efficacy/Toxicity
Toxicology
A model experiment:
Two samples of interest
EGFP expressing cells
EGFP KD
Differential
Gene
Expression?!
http://www.oardc.ohio-state.edu/plantranslab/gfp-a.gif
Q: Which genes are differentially expressed in EGFP cells versus EGFP KD cells?
3
Process of transcribing deoxyribonucleic acid to ribonucleic acid is
“TRANSCRIPTION”
RNA
Nucleic acids must be translated into amino acids that make up proteins
Process:
“TRANSLATION”
DNA
Cell
nucleus
Protein cytoplasm Chem.ox.ac.uk
Inside every cell: DNA
Serves as a genetic blueprint
Dna molecule: berkeley.edu
Relating Gene Expression
DNA
RNA
Protein
High throughput protein assays complicated We measure transcript level
Is a gene expressed?
Is protein produced
Ideally measure protein levels 4
Introduction
Two Popular Microarraying Platforms
Spotted microarrays
Commercially available microarray
www.molgen.mpg.de
cDNA: PCR products
(500-2,000bp)
synthesized oligos
>10,000 probes
www.the-scientist.com
Affymetrix
“Gene Chip”
500,000 probes
25 mer
Rebecca Fry, Ph.D.
http://www.buffalo.edu/UBT/UBT
What is a DNA Microarray? genes or gene fragments attached to a substrate (glass)
Tens of thousands of spots
Hybridized slide
Two dyes
Image analyzed
1
The Beginnings of Microarray Technology
Lockhart et al., 1996
Nature Biotechnology
“Expression monitoring by hybridisation to high-density oligonucleotide arrays” Schena et al., 1995
Science
“Quantitative monitoring of gene expression patterns with a complementary
DNA microarray”
8 years later
4162 references
2
Uses and Applications
Target identification
Pathway mapping
Gene screening
Mechanism of Action Studies
Disease characterization
Molecular Diagnosis of Disease
Personalized medicine
Developmental Biology
Prediction of Drug Efficacy/Toxicity
Toxicology
A model experiment:
Two samples of interest
EGFP expressing cells
EGFP KD
Differential
Gene
Expression?!
http://www.oardc.ohio-state.edu/plantranslab/gfp-a.gif
Q: Which genes are differentially expressed in EGFP cells versus EGFP KD cells?
3
Process of transcribing deoxyribonucleic acid to ribonucleic acid is
“TRANSCRIPTION”
RNA
Nucleic acids must be translated into amino acids that make up proteins
Process:
“TRANSLATION”
DNA
Cell
nucleus
Protein cytoplasm Chem.ox.ac.uk
Inside every cell: DNA
Serves as a genetic blueprint
Dna molecule: berkeley.edu
Relating Gene Expression
DNA
RNA
Protein
High throughput protein assays complicated We measure transcript level
Is a gene expressed?
Is protein produced
Ideally measure protein levels 4
Introduction
Two Popular Microarraying Platforms
Spotted microarrays
Commercially available microarray
www.molgen.mpg.de
cDNA: PCR products
(500-2,000bp)
synthesized oligos
>10,000 probes
www.the-scientist.com
Affymetrix
“Gene Chip”
500,000 probes
25 mer