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The DNA Microarray facility is intended for genetic analysis with applications to basic research as well as for structural and functional genomics. |
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OBJECTIVES |
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To establish the expression pattern in different disease causing parasites |
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To establish drug targets |
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To establish SNPs |
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To establish predictive toxicity models. |
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Microarray data analysis
An experiment with a single DNA chip can provide researchers information on thousands of genes simultaneously – a dramatic increase in throughput.
Once immobilized on the solid support, the genetic material can be used to interrogate samples of uncertain identity using traditional principles of nucleic acid hybridization. Microarrays are
used in three main activities:
1. Discovery of single nucleotide polymorphisms (SNPs)
2. Expression analysis
3. Comparative genome hybridization (CGH) studies
Steps Involved in DNA Microarray
Most DNA microarray applications employ a similar experimental approach, comprising
the following steps:
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Preparation of target DNA |
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Preparation of probe DNA |
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Hybridization |
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Signal detection and data analysis |
For microarray data analysis there are different criteria for classification and data usage patterns so we have standardized our procedure for ease of use and accuracy of results.
(after Scanned images and Raw data has been generated using our scanning service.)
Folowing are recommendations for data analysis :
| A media containing Images (with numbers/names) |
Scan conditions for each image file
(with numbers/ names corresponding to the Image files) |
| Raw data (not normalized) as generated by Genepix Pro. |
A word document/ excel file/tab limited text with the following data:
Experment number |
VS |
Sample description |
| Sample description |
Dye |
| Dye |
File name (should be common for Image/ raw data) |
Flip dye experiment of which experiment |
| Other info |
Analysis of data yields :
- Quality Control:
- Reproducibility of the data
- Major sources of error
- Gene List:
Gene Name |
Fold Change
(expt1) |
Fold Change
(expt2) |
Fold Change
(expt-n) |
Here exp means experiment and n denotes the number of experiments.
- Clusters with interesting Gene expression profiles
- List of genes in the clusters.
- Average expression profile of the cluster
- Description of the profile
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