What Is Microarray A new powerful technology for biological exploration Parallel High-throughput Large-scale Genomic scale
Jan 03, 2016
What Is Microarray A new powerful technology for
biological exploration Parallel High-throughput Large-scale Genomic scale
Microarray
ATATCGGCATCAGTCGATCGATCATCGATCGAT
UAUAGCCGUAGUCAGCUAGCUAGUAGCUAGCUA
ATATCGGCATCAGTCGATCGATCATCGATCGAT
DNA
mRNA
cDNA
DNA RNA Protein
Transcription
Reverse transcription
TranslationReplication
What Is Microarray Different Approaches
Stanford/Synteni
Affymetrix
How DNA sequences are laid down
Spotting Photolithography
Length of DNA sequences
cDNA(Complete sequences)
Oligonucleotides
Affymetrix Probe Array (Photolithography)
Synthesis of probe
Hybridization
Stanford Approach Use robot to spot glass slides Able to measure qualitatively relative
expression levels of genes Differential expression by use of simultan
eous, two-color fluorescence hybridisation
Cheaper with DIY ($60,000) Also called home-made system
Life Cycle(cont.)
Cy3(green)
Cy5(red)
Procedures Preparation
Target DNA (reference and test samples) Slides
Reaction(Droplet or Pin Spotting) Hybridization
Scanning Analysis
Image processing Data mining Modeling
ArrayerScanner
Hardware
Software
Instruments Arrayer Scanner
Laser Confocal Microscope
Arrayer
Scanner GenPix 4000
Problems – by direct view
Anti-probe Locally high background Spot overlap
Precipitate Locally low signal Comet-tails (donut hole)
Problems –related wit IP Local problems
Spot position variation Spot shape and size irregularity Spot Overlapping
Global problems High background Low signal White-noise/Speckle effect
(Contamination)
Array Alignment
Good Alignment Bad Alignment
Spot Finding Grid System Determination
Manual Semiautomatic Automatic
Spot Segmentation Space-based Intensity-based Frequency-based Hybrid approach
Grid System Determination
Spot Segmentation
Spot Segmentation(cont.)
Applications Gene expression studies
Gene function for cell state change in various conditions
Disease Diagnosis Pathogen Analysis
Applications(Cont.) Drug Discovery
identify appropriate molecular targets for therapeutic intervention
monitor changes in gene expression in response to drug treatments
Trageted Drug Treatment
Example Images – E. Coli
Example Images – C. Elegan
1.75
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Log(R/G)
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Gene index
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Log(R/G)
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Log(R/G)
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Log(R/G)
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N gene
M experiments
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