Microarray. DNA DNA can be manipulated to create exact copies that are extremely accurate. DNA is...
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Transcript of Microarray. DNA DNA can be manipulated to create exact copies that are extremely accurate. DNA is...
![Page 1: Microarray. DNA DNA can be manipulated to create exact copies that are extremely accurate. DNA is predictable and programmable. DNA also has the ability.](https://reader036.fdocuments.net/reader036/viewer/2022062518/5697bf741a28abf838c7f6e4/html5/thumbnails/1.jpg)
Microarray
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DNA
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• DNA can be manipulated to create exact copies that are extremely accurate.
• DNA is predictable and programmable.
• DNA also has the ability to store enormous amounts of information
Why DNA?
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DNA chips
• Based on genetic information • Based on DNA structure
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What is Microarray ?
• Microarrays are fabricated by high-speed robotics, generally on glass but
sometimes on nylon substrates, for which probes with known identity are
used to determine complementary binding, thus allowing massively
parallel screening studies.
• An experiment with a single DNA chip can provide researchers
information on thousands of genes simultaneously - a dramatic increase in
throughput.
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• In 1975, Ed Southern proved the concept that DNA fixed to a solid support could be used to attract complementary DNA strands in a process now known as Southern blotting.
• In 1991, Stephen Fodor at Affymax reported the fabrication of DNA microarrays on the surface of glass chips by combining the photolithographic method
• In 1993, he co-founded Affymetrix, in order to develop microarrays with hundreds of thousands of different oligonucleotides.
• Next year Affymetrix commenced manufacturingand selling its first DNA microarray, GeneChip, and the DNA microarray market was born.
• Pat Brown at Stanford University developed a method for mechanically arraying and immobilizing numerous PCR-derived cDNAs using a robot to print onto simple glass slides. [http://brownlab.stanford.edu/]
Microarray
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Types of Arrays – Applications:
• DNA Microarrays:
Expression profiles, disease research (cancer), DNA sequencing, mutation analysis, gene discovery, diagnosis, drug discovery,…
• RNA Microarrays:
RNA-protein interactions, biological function of proteins, drug discovery,…
• Protein Microarray (chips):
Enzyme profiling, Protein-protein Interaction, Protein-ligand interaction ,...
8
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Arrays
• Complementary DNAs (cDNA)• Amplicons• Oligonucleotides• Proteins
Arrangged on
• Nylon / Nitrocellulose• Glass • Silicon
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Probe production
Oligos (up to 60-80 nt)-synthesized on silica (Affymetrix)-synthesized and spotted, or sprayed (Agilent)
PCR products (100-500 nt)-produced by PCR from plasmid templates-purified and spotted
cDNA (1-5 kB)-clones expanded by bacterial cultures (1000s)-plasmid purified-spotted to substrate (nitro, plastic, glass)
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DNA chip classification
• Low density 10-1000 probes for diagnosis• Medium density 1000-10000 probe for mutation analysis• High density 10000-? probes for gene sequencing
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Microarray parameters
subarray
Slide
Gene/Protein
spot
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Selected parameters of DNA chips
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Array production
• In silica synthesis- Affymetrix (photomasking)- Nimblegen- density unlimited (>500K features/cm2)
• Spotting- robotic ‘quills’ or ‘loop and pin’- density limited by diffusion properties of
solution and substrate (16-32K/slide)• Spraying
- nano/picoliter sprays (inkjet, Agilent-H/P)
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Affymetrix Photolithography
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Febit/NimbleGen photolitography
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Slide surfacesP P P- - -
NH3 NH3
+ +NH3 NH3
+ +P P P- - -
1.Poly-L-lysine
2.Amin
3.Aldehyde
4.Epoxy
CH
=
ONH2 CH
=
N +H2O
CH
CH2 O
NH2
NH
CH
CH2
HO
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Robot Spotting
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Spotting of DNA library on slides
Microtiter plates Glass slides
3000 spots per slidePCR products
from >9000 genes
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InkJet (HP/Canon) technology
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Plate with wellscontaining probes
microarray slides
vacuumwashstation
Cartoon of Printing Process)side view from the table top(
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Dip pen Nanolithograph
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Micro scale array Nano scale array
Today Tomorrow
3 μm 3 μm
Future
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Process of the Microarray experiment
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Detection methods
•Radioactive- incorporate 32P-CTP into RT step- sensitive, but nearly obsolete
•Fluorescent- single color, or 2 color (Cy3, Cy5)- 2 color allows 2 samples on 1 chip
•Antigenic- hybrid capture uses antibody to Double strand
•Electrochemical- circuit sensing
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•Electrochemical Sensing•Principle•Oxidation/Reduction
e-
“Electrons flow from the AuElectrode to intercalated MB+ andThen are accepted by the Fe(CN)6
4-”E.M. Barton, J.K., N.M. Hill, M.G (1999) NucleicAcid Research 27, 4830.
e-
e-
e-
Electrochemical Sensing(cont)
•Combination of Biological and Electrical chips
Proposed Chip Concept
Circuitry
A
e-
e-
e-
Nano DNA Array
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Hybridization
GeneTAC Hyb station
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Image processing by Laser scanning
The microscope slide containing the microarray is placed inside a microarray scanner, where the slide is scanned with two lasers to detect the bound green and red cDNAs.
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Microarray Data Analysis
How to Handle Microarray Data?
• Signal Generation from Image
• Normalization
• Filtering
• Statistical Tests
• Clustering
The Main Goal of Microarray Data Analysis is to Generate aList Of ‘Interesting’ Genes
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Image Analysis
1. Gridding: identify spots (automatic, semiautomatic, manual)
2. Segmentation: separate spots from background
3. Intensity extraction: mean or median of pixels in spot
4. Background correction: local or global
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Image Analysis
• Spot Finding
• Background subtraction
• Intensity Calculation
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Background subtraction
● Global background
● Local background
● Negative control
● Morphological opening
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Data analysis
What accounts for the varying colors?
These actually correspond to the amount of cDNA that binds to the complementary strands on the spot.
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Data analysis
Merged images
Induced RepressedExpressed in
both conditions
R G
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Expression ratio - Normalization
R
GT=
Reference/ Control
Test/ Experimental
1800011600 13000 1550056001200600
8002500650010900135001650017500
22.56.22.01.00.40.070.03
R
G
0/0
∆Gene expression
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Reporting your results
Microarray
Gene
The expression ratios for every gene can be organized into a table where each column is a microarray and each row is a gene. This representation however is overwhelming in experiments involving thousands of genes and data.
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Gene expression microarray
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43
Using cDNA Microarrays to Measure mRNA Levels
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
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Sample 1
Sample 2
Microarray Slide
Spots(Probes)
UnknownmRNA
Sequences(Target)
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44
Extract mRNA
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
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Sample 1
Sample 2
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45
Convert to cDNA and Label with Fluorescent Dyes
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
Sample 1
Sample 2
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Sample 1
Sample 2
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46
Mix Labeled cDNA
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
Sample 1
Sample 2??????????
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47
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
Sample 1
Sample 2
Hybridize cDNA to the Slide
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48
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
Sample 1
Sample 2
Excite Dyes with Laser
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49
ACCTG...GACCTG...GACCTG...G
TTCTG...ATTCTG...ATTCTG...A
GGCTT...CGGCTT...CGGCTT...C
ATCTA...AATCTA...AATCTA...A
ACGGG...TACGGG...TACGGG...T
CGATA...GCGATA...GCGATA...G
Sample 1
Sample 2
Scan
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50
Quantify Signals
ACCTG...G
76527652138138
TTCTG...A
5708570843884388
GGCTT...C
85668566765765
ATCTA...A
120812081344213442
ACGGG...T
6784678497629762
CGATA...G
6767239239
Sample 1
Sample 2
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Comparative genomic hybridization CGH array
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Chip-on-chip
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Tiling array
Partially overlapping probes
Non overlapping probes
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Genome Tiling Arrays
800 bp
25-36mer
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http://www.mged.org/Workgroups/MIAME/miame.html
•Array Design•Experimental Design
•Samples used, extract preparation and labelling •Hybridization procedures and parameters
•Measurement data and specifications of data processing
MIAMIMinimum Information About a Microarray Experiment
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Illumina BeadArray
Miller M B , Tang Y Clin. Microbiol. Rev. 2009;22:611-633
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Illumina Bead Arrays• Oligonucleotides (50-
mers) immobilized on glass beads
• Identifier tag on each oligo
• Usually ~ 30 beads per probe
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The promise of the protein microarray is the ability to interrogate a large number of proteins simultaneously in a high-density format for disease diagnosis, prognosis or efficacy of therapeutic regime as well as for biochemical analysis
Protein arrays
A new tool on behalf of traditional macroscopic technology such as 2 dimensional electrophoresis, mass spectroscopy (MS), capillary electrophoresis (CE), and enzymelinked immunosorbent assay (ELISA)
The protein chip, although analogous to DNA chip, faces much great challenges in terms of commercial product. This systematic analytical device for proteome study requires biological surface fabrication to retain the activity of immobilized protein, miniaturization of protein array, and detection technology with high sensitivity.
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60
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Why study proteins?
• They are the machines that make cells function.
• RNA levels do not always accurately predict protein levels.– Often processes are regulated at the transcriptional level.– Some processes are controlled post-transcriptionally.
• Proteins are the targets of drugs.
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Protein-protein array
Different type arrays
Protein-activity array
Small molecule array
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Methods of synthesis
• In-situ synthesis
• Nucleic acid programmable protein array (NAPPA) • Protein in situ array (PISA)
• In situ puromycin-capture
• Nano-well array format
• DNA array to protein array (DAPA)
• Printing
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Nucleic acid programmable protein array (NAPPA)
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Protein in situ array (PISA)
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In situ puromycin-capture
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Nano-well array format
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DNA array to protein array (DAPA)
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-Perform synthesis without pre-assembly amplification
-Enables increased utilization of high-density DNA microarrays by:
-reducing pool complexity-limiting undesired oligo interactions
-maintaining reagent concentrations at desired levels
Integrated Microarray-Microfluidics
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SNP-array and gene expression DNA microarray data mapped to chromosomal positions.
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Use of SNPscanPlot to visualize chromosomal anomalies in apparently normal individuals.