1. What are the Advantages?
Microarray
What can it be used for?
How does it work?
What are the Advantages?
An Example Application
Current version
I the past Biologist have followed a one gene one experiments philosophy. Today with new technology of microarrays scientist can investigate the expression of several genes at once using this high throughput method. This provides the potential to monitor thousands of genes at the same time.
Hybridization is the fundamental concept of how this works.
Impacting many fields like genomics, drug discovery, and toxicological research.
Currently cost is high. Demand, competition and time will bring down the costs.
Most used for RNA expression levels.
Get differences between oligonucleotides and cDNA methods.
Arrays with 5,000 to 10,000 genes are common.
The challenge is in
The main use is for comparison of expression analysis.
oligonucleotides method;
Photolithography is used to construct arrays with high information content onto glass slides. The slides are turned upside down over the hybridization chamber so that fluorescently tagged nucleic acids can hybridized. The laser if focused through the back of the glass to the target solution. The fluorescence emission is collected by a lens and passed through filters to the detector. The array may be moved or the laser or both.
Used to understand under what conditions and to what level the gene is expressed.
cDNA methods;
Gene-specific polynucleotides are arrayed on the matrix. The matrix is probed by fluorescently tagged cDNA made from the expressed RNA.
Printing Methods;
Robot used to place material on slide.
Contact method.
Non-contact, capillary tube, ink-jet being tried.
The DNA is cross-linked to the matrix by UV light to fix it. Some of the DNA is changed to single-strand by heat or alkali.
RNA is used as template to make cDNA by reverse transcription using fluorescence labeled nucleotides.

2. Microarrays can be used for:
Comparison of transcription levels between two cells
Examples:
Comparison between:
Cells from a young mouse vs cell from an old mouse
Drug efficacy:
Treated cells vs untreated cells

3. Based on hybridizationG A C U G A
mRNA
How it works:
Based on hybridization U G A C A C T G ▀
A =
C ≡
T =
G ≡ ▀ U G A C
A =
C ≡
T =
A ≡ ▀ U G A
A =
C ≡
T =
A ≡ ▀

4. Probes and the printing process
Head
slides (100)
Microtiter
Plates

5. Pins Print Head Printing Methods;
Robot used to place material on slide.
Contact method.
Non-contact, capillary tube, ink-jet being tried.
The DNA is cross-linked to the matrix by UV light to fix it. Some of the DNA is changed to single-strand by heat or alkali.

7. The printing tips is like a foutain tip pen
The printing tips is like a foutain tip pen. They are machined in a way that promotes capillary action. Liquid is drawn into the tip by putting it into DNA solution in a 96-well plate. The drops are also formed by capillary action, and the size of the drops are determined partly by the sharpness of the point. Printing is performed by lowered the tip very close the surface of the slide.

9. Print Head with Pins

11. Comparative Hybridized Experiment
The goal of comparative cDNA hybridization is to compare gene transcription in two or more different kinds of cells.
Regulatory Gene Defects in Cancer
Genetic disease is often caused by genes which are inappropriately transcribed -- either too much or too little -- or which are missing altogether. Such defects are especially common in cancers, which can occur when regulatory genes are deleted, inactivated, or become constitutively active. Unlike some genetic diseases (e.g. cystic fibrosis) in which a single defective gene is always responsible, cancers which appear clinically similar can be genetically heterogeneous. For example, prostate cancer (prostatic adenocarcinoma) may be caused by several different, independent regulatory gene defects even in a single patient. In a group of prostate cancer patients, every one may have a different set of missing or damaged genes, with differing implications for prognosis and treatment of the disease.
Comparative hybridization serves two purposes in the study of cancer: it can pinpoint the transcription differences responsible for the change from normal to cancerous cells, and it can distinguish different patterns of abnormal transcription in heterogeneous cancers. Understanding the diverse basis of a cancer is crucial for inventing therapies targeted to the different varieties of the disease, so that each patient receives the most appropriate and effective treatment.
Cancers are common examples of genetically heterogeneous diseases, but they are by no means the only ones. Diabetes, heart disease, and multiple sclerosis are among the diseases for which genetic risk factors are known to be heterogeneous

12. The normal gene is shown in all blue nucleotides
The normal gene is shown in all blue nucleotides. Sequences that have black letters are the nucleotides positions that are mutants.
oligonucleotides method;
Photolithography is used to construct arrays with high information content onto glass slides. The slides are turned upside down over the hybridization chamber so that fluorescently tagged nucleic acids can hybridized. The laser if focused through the back of the glass to the target solution. The fluorescence emission is collected by a lens and passed through filters to the detector. The array may be moved or the laser or both.

15. This slide shows the spot fluorescing and an example of smearing of the fluorescing material.

16. This is a zoom on the spots fluorescing not the red and green and the level of each.

21. Breast Cancer example from The New England Journal of Medicine Title
GENE-EXPRESSION PROFILES IN HEREDITARY BREAST CANCER
INGRID H EDENFALK , M.S., DAVID DUGGAN , PH.D., YIDONG CHEN, PH.D., MICHAEL RADMACHER, PH.D.,MICHAEL BITTNER, PH.D., RICHARD SIMON, D.SC., PAUL MELTZER, M.D., PH.D., BARRY GUSTERSON, M.D., PH.D.,MANEL ESTELLER,M.D., PH.D., OLLI-P. KALLIONIEMI, M.D., PH.D., BENJAMIN WILFOND, M.D., AKE BORG, PH.D.,AND JEFFREY TRENT, PH.D.