Microarray-gene expression analysis

1. Prepared by:
Bharatesha .S
8th sem
2014-2015
Guided by:
Dr.Amruthavalli

2. CONTENTS
Introduction
A brief history about DNA microarray
 Three basic aspects of DNA microarray
-Coupling of oligonucleotides to a platform
- Preparing samples for detection and Hybridization
-Scanning and analysing the data
Applications
Limitations
Conclusion
References

3. INTRODUCTION
A DNA microarray (also commonly known as DNA chip or biochip).
DNA microarrays use gene sequencing and DNA transcription and
hybridization to analyze and identify thousands of genes simultaneously.
Scientists use DNA microarrays to measure the expression levels of large
numbers of genes simultaneously or to genotype multiple regions of a
genome.
DNA micro array is a set of oligonucleotide sequences representing
the entire set of genes of an organism, arranged in a grid pattern .

4. A BRIEF HISTORY ABOUT MICROARRAY TECHNOLOGY
(1991)
Patrick Brown(1992) David.R.Walt (1998)

5. Coupling of oligonucleotides to a platform(DNA microarray fabrication)
1) Inject printing fabrication
 In this method high density DNA arrays to be made on glass substrate.
 The diameter of the nozzles is in the micrometre scale.(1-100μm)
 Accurate volume of solution at Pico litre ,spotted on to a microscopic
slide
Microarrayer Inkjet printhead

6. Development of a 3-Axes Robotic System for Making DNA Microarrays
Bhabha Atomic Research Centre

7. 2) Affymetrix gene chip technology
 This method was first developed by Affymetrix Inc., company.
 Here oligonucleotides are synthesized on a silicon chip using
photolithographic method.
 Each features on a gene chip may be as small as 50 nm square.
 Affymetrix uses several photo masks and lighting process to expose
reaction positions selectively on silicon plates, then attaching oligos on
to it.

9. Protect Deprotect
Add

10. Array of oligonucleotides
Gene chip

11. Preparing samples for detection and hybridization
 RNA is extracted from two different samples and converted in to cDNA ,
during which the cDNA is labelled with fluorescent compounds.
 The two samples are then mixed together for comparison and hybridised
to the array.

12. Interpretation of microarray result
 After hybridization is complete, each feature of a microarray grid is
scanned by a green laser and a red laser to detect the presence of both
control and test DNA hybridization .
A fluorescing DNA microarray showing the result of DNA hybridization
between the probe and target DNAs.

13. Applications of DNA microarray
 Sequence analysis
 Gene expression analysis: gene discovery
 Identification of single nucleotide polymorphism
 Whole genome association studies

14. Limitations of DNA microarray
 The complexity of biological systems
 The tissue sample
 Microarray analysis will not detect certain chromosome rearrangements
 We need to know in advance which genes we are looking for.
 Non coding RNAs could not be analysed with this method

16. REFERENCES
 DNA microarray learning module,
Southwest centre for microsystem education,
New Mexico.
website: www.scme-nm.org
 Roger Bumgarner, DNA microarray : Types, Application and their future,
current protocol molbio,2013 January, University of Washington.
 http://www.ncbi.nlm.nih,gov/pmc/articles/PMC2659835

17. ACKNOWLEDGEMENT
I would like to thank my guide Dr. Amruthavalli for her
valuable guidance and also our course coordinator Dr.
N.S.Devaki for giving me this opportunity to present
my seminar.
Thank you all .