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EASY TO USE MICROARRAY PRODUCTS-TODAY!
Pat Mayer
Global Product Manager
MICROMAX Feb. 2002
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PerkinElmer Microarray Solution
Spotters
Data Analysis Software
GeneTAC G3
Glass Slides
Scanners
Slide Scanning Service
PerkinElme
r
Genomics
NEN Brand Nucleotide
Analogs (Cyanine- and
Biotin-labeled)
GeneTAC Hybstation
Labeling Kits
Prespotted Microarrays
Complete Microarray Systems
PerkinElmer Microarray Solution
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Why MICROMAX Products?
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Why MICROMAX Products?
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Differential gene expression
Gene expression
Relative levels of RNA and proteins
Differential gene expression
Differences in levels of RNA and proteins as a result of changes
in cellular phenotype
Backgound MICROMAX Technology
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Backgound MICROMAX Technology
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Microarrays

A new and prominent technology that vies with
PCR as the most significant commercial scientific
advance of the decade.
Technology allows
Miniaturized format
Membrane or glass slide
Detection instrumentation
Analysis software
Backgound MICROMAX Technology
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DNA Microarrays
 Membrane Arrays
 Oligonucleotide Arrays
 cDNA or Long Oligo Arrays
Backgound MICROMAX Technology
Types of DNA Arrays
Membrane Arrays
cDNA spotted on nylon membrane
Rad nucleotides (chemiluminesence)
Gene expression and novel gene discovery
Advantages
Standard molecular biology techniques
Sensitive
Reusable
Unknown genes (ESTs) can be analyzed
Disadvantages
Single analysis per array
Low density
Radioactive safety
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Backgound MICROMAX Technology
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Types of DNA Arrays
Oligonucleotide chips
Oligo probes synthesized onto chip
Fluorescence detection
Gene expression and mutational analysis
Advantages
Very specific, can identify isotypic changes or SNPs
Tens of thousands oligos can be analyzed per chip
Automation
Disadvantages
Only known genes can be analyzed
Single analysis per array
Low sensitivity
Many spots make a gene
May be too specific for gene expression analysis
Not reusable
Backgound MICROMAX Technology
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Types of DNA Arrays
Glass microarrays
cDNA or long oligos (50-70 mers) printed onto slides
Two-color fluorescence detection
Gene expression and novel gene discovery
Advantages
Dual detection for accurate differential analysis
Thousands of individual cDNA per slide
Unknown genes (ESTs) can be analyzed
Automation
Disadvantages
Low sensitivity
Not reusable
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Backgound MICROMAX Technology
Labeling and detection for Microarrays
Direct - radioactivity
Reverse
Transcriptase
mRNA
33P
dNTP
*P*
*P*
cDNA
Preferred method for membrane arrays
** Single detection , Very sensitive**
*P*
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Backgound MICROMAX Technology
Labeling and Detection for Microarrays
Direct - fluorescence
Reverse
Transcriptase
mRNA
fluoro- dNTP
F
F
F
cDNA
Standard method for glass and oligo arrays
** Dual detection, Good sensitivity**
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Backgound MICROMAX Technology
Labeling and Detection for MICROMAX
Indirect and amplified - Fluorescence
F
F F
T F T T
T
H
H F H
F
T
T
B
B
B
Y
biotin-dNTP
fluorescein-dNTP
Y
mRNA
Y
Reverse
Transcriptase
cDNA
Excellent method for glass arrays (MICROMAX-TSA)
** Dual detection, Excellent sensitivity**
TSA Technology Review
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TSA Technology Review
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TSA is a proprietary, PATENTED technology developed at
NEN
Patented under the name CARD (Catalyzed Reporter Deposition)
Commercialized under the name TSA (Tyramide Signal Amplification)
TSA Technology Review
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Keys To TSA
Inroduction of Horseradish Peroxidase (HRP) enzyme
Labeled Tyramide
TSA Technology Review
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SIGNAL AMPLIFICATION
SIGNAL AMPLIFICATION
SIGNAL AMPLIFICATION
TSA Technology Review
SENSITIVITY
SENSITIVITY
SENSITIVITY
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TSA Technology Review
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Signal Detection

Used existing patented and proprietary technology
Amplify
TSA
Tyramide Signal Amplification
React with Tyramides
H
Y
Sample immobilized to a surface - slide
H
Y
Specific binding with
hapten containing probe
H
Y
Incubate with HRP- conjugate
B
B
B
TSA on Microarrays
Simultaneous hybridization
both Fluorescein and Biotin
labeled total RNA
Incubate with Anti-F-HRP
Amplify with TSA-cyanine 3
Inactivate Residual HRP
Incubate with streptavidin-HRP
Amplify with TSA-cyanine 5
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Sequential Fluorescence
Deposition with TSA
TSA Technology Review
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Reduced Customer Sample Requirements
TSA reduces the input RNA sample up to 200-fold
Increases opportunity for microarray technology use
Tumor samples
Reduced RNA sample costs
Increased # of experiments
MICROMAX microarray Analysis with Direct Fluorescence
and Tyramide Signal Amplification
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4800 Slide
Direct Labeling Method
TSA Labeling Method
(100 µg Total RNA)
(1 µ g Total RNA)
TSA labeling method is very sensitive and needs as little as 0.5 to 1 µ g total RNA
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Direct and TSA Labeling: Scatter Plots
Direct
TSA
10000
Jurkat: Cyanine 3
Jurkat: Cyanine 3
10000
1000
100
10
1000
100
10
1
1
0.1
0.1
SA177_Direct_Cy5_P67_L80 data.gpr (control)
0.01
1
10
100
1000
HL-60: Cyanine 5
10000
SA197_TSA_Cy5_P65_L45 data.gpr (control)
0.01
1
10
100
1000
10000
HL-60: Cyanine 5
TSA labeling method is highly sensitive and identifies more differentially
regulated genes
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MICROMAX Platforms
Fully integrated systems for streamlined
application and consistent performance.
tissue samples
isolate
total RNA
cDNA
labeling
Cyanine 3/5
dNTPs
OR
hybridize
imaging
data analysis
Biotin/Fluorescein
linked
dNTPs
hybridize
TSATM amplified
fluorescence detection
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MICROMAX Products and Services = Flexibility
Reagent Kits
Slide Scanning and Data
Processing Services
TSA Kit
Direct Kit
Microarray Products
Cyanine 3- labeled dCTP, dUTP
Cyanine 5- labeled dCTP, dUTP
Complete
Microarray Systems
Quality Control microarray
(Practice Slide: 25 genes)
Human Screening microarrays
MICROMAXTM TSA
Microarray Systems
MICROMAXTM Direct
Microarray Systems
Human Screening Array System I&II
Human Array Systems I&II
Human Focused microarrays
Glass Slides
ULTRACLEAN I
SUPERCHIP I
Human Focused Array Systems
Chemical Labeling Kit
System Components
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MICROMAX Direct
MICROARRAY SLIDES
2 human cDNA
microarrays
2 practice arrays
coverslips
cDNA PREPARATION
Cyanine 3-dUTP
Cyanine 5-dUTP
Reverse Transcriptase
(RT)/RNase inhibitor
dNTP labeling mix
Unlabeled control RNA
HYBRIDIZATION
Hybridization Buffer
INSTRUCTION MANUAL
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System Components
MICROMAX TSA
MICROARRAY SLIDES
2 human cDNA
microarrays
2 practice arrays
coverslips
cDNA QC CHECK AND HYBRIDIZATION
Biotin- and Fluorescein-Control cDNAs
GeneScreenTM Membrane
Streptavidin-HRP and Anti-Fluor HRP
Hybridization Buffer
cDNA PREPARATION
Biotin and Fluorescein
Nucleotides
dNTP Nucleotide Mix
Reverse Transcriptase
(RT)
RNase Inhibitor
Unlabeled control RNA
DUAL FLUORESCENCE
DETECTION
TSA Amplification Buffer
Cyanine 3-Tyramide
Cyanine 5-Tyramide
HRP Inactivation Reagent
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Platform Specifications
MICROMAX Direct

Sample Requirement
MICROMAX TSA

• 20-80 ug Total RNA

Dynamic Range
• 0.5-1 ug Total RNA

• 8-125,000 pg input mRNA
(>104)

Differential Sensitivity
•  2-fold ratio difference
Sample Requirement
Dynamic Range
• 0.04-200 pg input mRNA
(>103.5)

Differential Sensitivity
•  3-fold ratio difference
MICROMAX Products & Services
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Complete MICROMAX Systems
MICROMAX Human cDNA Microarray System I-Direct
Direct Fluorescence Labeling System
5 slides
MICROMAX Human cDNA Microarray System 1.1-TSA
TSA Fluorescence Labeling System
5 slides
MICROMAX Human cDNA Microarray System II-TSA
TSA Fluorescence Labeling System
5 slides
Positioning
Everything for novice microarray user
MICROMAX Products & Services
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MICROMAX Reagent Kits
MICROMAX Direct Reagent Kit
Direct Fluorescence Labeling Kit
10 Labeling Reactions
50 Labeling Reactions
MICROMAX TSA Labeling and Detection Kit
TSA Fluorescence Labeling Kit
10 Labeling & Amplifcation Reactions
40 Labeling & Amplifcation Reactions
Positioning
Researchers who manufacture their own microarrays
MICROMAX Products & Services
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MICROMAX Pre-Spotted Microarrays
MICROMAX Microarray:
MICROMAX Microarray:
MICROMAX Microarray:
MICROMAX Microarray:
Human cDNA 1.1 (2400 human genes)
Human cDNA II (4800 human genes)
Quality Control Slides
Focused Array Slides (~270 human genes)
2 Microarrays
GeneMAP Microarrays: Human, Mouse and Rat
5 microarrays
Positioning
Experienced researchers who don’t have access to
cDNA arrays
Experienced researchers who have their own labeling
technology
MICROMAX Products & Services
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MICROMAX Slide Scanning Service
Scanning of all types of MICROMAX Slides
Practice Arrays free of charge
Slide Scanning Service Upgraded
Web Based Service
Positioning
Novice researchers who don’t have access to
fluorescent microarray scanner
Selling GeneMAP Microarrays

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What are they?
• Spotted, preprinted arrays
• Human, mouse and rat glass microarrays

Available Worldwide (non-exclusive) from
PerkinElmer

Sales of GeneMAP will count towards your MM sales
goals!
• Under a different pac code however, 2063
MICROMAX Competition
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MICROMAX Competition
Who sells “Complete Systems”?
Labeling System
Nucleotides
Slides
ONLY PERKINELMER!
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MICROMAX Competition

Competition
Company
Labeling Kits
Slides
Affymetrix
x
X
Agilent
Clontech
Amersham
Stratagene
Genisphere
Mergen
X
X
X
X
HOMEBREW!!!!
X
X
X
X
X
X
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MICROMAX Competition
Competing Technologies
cDNA Labeling Technology
AminoAllyl
Clontech
Dendrimer
Genisphere
HOMEBREW
Slide Technology
Short (20-30 mers) Oligo
Affymetrix
Mergen
Medium (70-80 mers) Oligos
Clontech
cDNA
Agilent
Takara
HOMEBREW
MICROMAX Competition-Technologies
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Aminoallyl labeling technology…….
Amino groups are incorporated during cDNA synthesis using
aminoallyl-dUTP
Cy3 or Cy5 monomer NHS ester is reacted with cDNA
Labeling is independent of incorporation of dye-dNTP analogs
……is a novel technology which is cumbersome
TARGET CUSTOMER FOR NEW CHEMICAL LABELING!
MICROMAX Competition-Technologies
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Genisphere’ s dendrimer technology…...
Labeling of cDNA RT with Unlabeled deoxynucleotides and Cy3™
or Cy5™ Primer Oligo (=3DNA Capture Sequence)
Hybridize to Array
Detect with 3DNA Fluor (Complementary Capture Sequence
labeled with Cy-Dye™)
…...only competing technology to MICROMAX-TSA
Our customers have told us this doesn’t work very well-no specific signal
Competitive Advantages

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Low cost entry to microarray technology
Every lab can afford it!

Complete systems right out of the box
Easy to use!

Broad product offering
Something for every lab!

License to do dual color fluorescence hybridization
Two samples on one slide!
MICROMAX Selling
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Probing Questions…...
Are you currently using microarray technology in your research?
Do you anticipate using microarray technology in the near future?
Is your differential gene expression research limited by the amount
of starting material?
Are you just getting started in microarray technology?
…….leads to providing customers with the right products
QC Process for Microarray products

Labeling and Detection Kits
• QC all components
• Nucleotides HPLC QC
• Nucleotides functional
testing
• Components used in
functional testing of
microarrays
• Cross check in R & D and
Applications Lab

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Microarrays
• Check PCR process
– In process checks
• Check autofluorescence of
glass slides
• Representative sequencing
• Check after printing for
spots
• Functional testing of arrays
– Spot morphology
– Spot size
– S/N
• Cross check in R & D and
Applications Lab
New MICROMAX products in the last year

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4800 Arrays and Systems (1.1) (Alphagene genes)
• Now manufacture our own arrays
• TSA and Direct versions

Direct Kit
• more economical-$40/slide

Focused Arrays
• Human Apoptosis & Neurobiology

Additional Screening Arrays and System (II)
• Incyte Genomics’ Gene Content

Coming Soon
• Glass Slides for DNA spotting
• New Chemical Direct Labeling System
• Mouse and Rat Screening Arrays
– Content from LION bioscience
• Control Kits
NEW
Current MICROMAX Ads

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MICROMAX TSA
• “The NEN TSA Microarray Labeling and Detection Kit lets you do
more with less”
• Ran about 10 times in 2001-will be redesigned

MICROMAX Direct Kit Ad
• “Simply the best microarray reagents on earth (or anywhere else
you would care to explore!”
• Ran about 2 times in 2001 and continue in 2002

MICROMAX Microarray Ad
• “A long time ago. . .in a galaxy far away. . .we started making prespotted microarrays. . .We Still Do.”
• Newly created and will run in 2002

MICROMAX Glass Slide Ad
• “We have a new addition to the family. . .Introducing MICROMAX
Glass Slides”
• Newly created and will run in 2002

MICROMAX Chemical Direct Labeling Ad
• Not created yet and will run in 2002
Introducing MICROMAX Glass Slides


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ULTRACLEAN I
• Glass Slides that are cleaned!
• For homebrew coating procedures
– Looking for evaluators (e-mail Pat)
– MPS692
Ultra-flat
Low Intrinsic Fluorescence
SUPERCHIP I
• Amino Coated Glass Slides
– Looking for evaluators (e-mail Pat)
– MPS695-5 slides
– MPS696-20 slides
Bundling opportunities with PerkinElmer printers and spotters!
Packaged in sets of 5 slides
Ready to ship evals February 11, 2002
Ready to ship by end of February
Breadth of Technical Support

In-field dedicated genomics specialists

Internal dedicated Technical Support
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• Leslie Stern X9117

Internal dedicated Applications Lab
• Testing and expanding microarray protocols

Research and Product Development Staff
• Organized for efficiency and time to market improvements
• External seminar series
MICROMAX Sales Tools Available
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MICROMAX Seminar
Will be updated ASAP to incorporate Packard instruments
MICROMAX Literature Pieces
Code
Name of Piece
H78255
H78511
P10208
H78414
H78381
H78416
MICROMAX
MICROMAX
MICROMAX
MICROMAX
MICROMAX
MICROMAX
Sell Sheet
TSA BioTechniques Reprint
Direct Reagent Kit Sell Sheet
TSA Sell Sheet
Focused Array Sell Sheet
TSA Protocol Laminated Card
Laminated card (H78416) is a must have for wet labs!
Order at www.perkinelmerliterature.com