Lecture 4 - Microarray Flashcards
Define Microarray
Collection of DNA fragments immobilized as microscopic spot (<200um) which allow quantitative analysis of thousand of genes through hybridization to a set of specific probes.
Application of Microarray
Expression Profiling Studies
-provide prognostic and predictive information
Comparative Genomic Hybridization (CGH)
- high resolution tool for screening CNV
- several advantage over classical karyotyping techniques
Important in evaluation and monitoring of drug safety
-ex. Amplichip CYP450- predict response to drug
Drug discovery, toxicology, and stem cell research
Detection of food-born pathogen
Types of microarray
- depend on how they have been manufacture
- depend on application that microarray are designed
Depend on how they have been manufacture;
- Spotted
- Synthesized
- Self-assembled
Depends on application that microarray are designed;
- DNA
- Expression
- SNP
- Tissue
- microRNA
- Protein
- Metabolite
Microarray Synthesis
- First layer of nucleotide is deposited to activated microarray surface by means of non-contact printing
- Growth of oligonucleotide is obtained by multiple rounds of base by base printing
- Close-up of one oligonucleotide as a new base is added to the chain.
- Final product is an array with thousands of copies of each probe which consist of long (60-mer) oligonucleotide.
Microarray Experiment
Formulate the research question ⤵️ Prepare the samples and label with fluoresceins ⤵️ Perform microarray hybridization ⤵️ Detect, Scan, Visualize, Analyze data ⤵️ Reach biological conclusion
Gene Expression Profiling
Tissue isolation ↪️ RNA Extraction ↪️ cDNA Synthesis ↪️ Target labeling ↪️ Hybridization data read out
Microarray experiments for differentiating gene expression uses two fluoresceins such as Cy3 (green) and Cy5 (red)
Analyzed by using scatter plot and significance of gene expression can be assed by T-test
