1. Webinar
High-Performance Cell-Based
Assay and qPCR Technologies
for Pathway-Focused Research
Louis Lichten, PhD
Application Scientist
5.10.12
For Internal Use Only
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Sample & Assay Technologies
2. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
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Sample & Assay Technologies
3. Systems Biology at QIAGEN
Research
DNA
RNA
Gene Expression
Protein
Gene Function
Protein Function
For Internal Use Only
SABiosciences™ Products
Somatic Mutation Arrays
EpiTect ChIP-qPCR Assays
Methyl-Profiler qPCR Arrays
Genomics Service Core
Discovery
Screening
Confirmation
Genomics &
Regulation
Technologies
Mutation Analysis
ChIP
Methylation
SNP/CNV
Genomics Service Core
RT2 PCR Arrays
miScript miRNA Arrays & Assays
RT2 qPCR Assays
Detection
Knockdown
Reporter System
Phenotypes
Cignal Reporter System
ELISArray Kits
siRNA Arrays / shRNA Plasmids
Phosphoprotein Quantitation Kits
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Sample & Assay Technologies
4. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
-4-
Sample & Assay Technologies
5. Anatomy of a PCR Array
84 Pathway-Specific
Genes of Interest
5 Housekeeping Genes
Genomic DNA
Contamination Control
Reverse Transcription
Controls (RTC) n=3
Positive PCR Controls
(PPC) n=3
96 well version (1 sample/PCR Array)
(384 well version available (4 samples/PCR Array)
For Internal Use Only
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Sample & Assay Technologies
6. RT2 Profiler PCR Arrays
cDNA Synthesis
45 minutes
.
Load Plates (Preferably with 8Channel Pipettors)
2 minutes
Automated Solution = QIAgility
.
Run 40 cycle qPCR Program
2 to 2.5 hours
Compatible with all major
Real Time PCR Instruments
.
Upload and Analyze Data
15 minutes
.
For Internal Use Only
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Sample & Assay Technologies
7. PCR Arrays for All Biomedical Researchers
Cancer and Apoptosis
Cytokines & Inflammation
Development & Stem Cells
Apoptosis
Inflammatory Cytokines
Stem Cells
Cell Cycle
Th17 for Inflammation (NEW!)
Wnt Signaling
Human miRNA Array (NEW!)
Common Cytokines
Notch Signaling
Breast Cancer & Estrogen Receptor
Chemokines
TGFβ / BMP Signaling
Tumor Metastasis
NF-κB Signaling Pathway
Endothelial Cell Biology
Cancer PathwayFinder
Th1-Th2-Th3
Osteogenesis
Angiogenesis
TNF Ligands
Growth Factors
Cancer Drug Resistance
Toll-like Receptors
ECM & Adhesion
Signal Transduction
Toxicology & Drug Metabolism
Neuroscience
Signal Transduction PathwayFinder
Drug Metabolism
Neuroscience Ion Channels
NFkB Signaling
Drug Phase I Enzymes
Neurotransmitter Receptors
Jak / Stat Signaling
Drug Transporters
Neurotrophins & Receptors
DNA Damage Signaling
Oxidative Stress
Neurogenesis and Neural Stem Cell
Insulin Signaling
Stress & Toxicity
MAP Kinase Signaling
Other Diseases
Custom PCR Arrays
cAMP / Calcium Signaling
Atherosclerosis
96-Well Custom Arrays
p53 Signaling
Diabetes
384-Well Custom Arrays
Complete PCR Array List
For Internal Use Only
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Sample & Assay Technologies
8. Accessing PCR Array Content
For Internal Use Only
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Sample & Assay Technologies
9. PCR Array: Functional Gene Groupings
For Internal Use Only
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Sample & Assay Technologies
11. miScript miRNA PCR Arrays
Complete miRNA genome (miRNome)
miScript miRNA Pathway Arrays
Human miScript miRNA PCR Array
Mouse miScript miRNA PCR Array
Rat miScript miRNA PCR Array
Dog miScript miRNA PCR Array
Species
Number of
assays
Human, Mouse, Rat:
Brain Cancer
Cancer
Cell Differentiation & Development
Immunopathology
Inflammation
miFinder
Neurological Development & Disease
Serum & Plasma
Total Number of Plates
(miRBase V16)
96 well
format
384 well
format
Human
1068
12
3
Mouse
947
12
3
Rat
653
8
2
Dog
277
4
1
For Internal Use Only
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Sample & Assay Technologies
12. Custom PCR Arrays – VERY POPULAR!
Analyze the Genes Most Important
To Your Research
• Same reliable and convenient
PCR Array product format
• 2 to 3 week turn around time
• Upload and Analyze Data, just like
our cataloged arrays
For Internal Use Only
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Sample & Assay Technologies
13. PCR Array Species Expansion
Species
Cataloged
Array
RNA QC
Array
HKG Array
Custom
Array
Individual
Primer Assays
Human
Y
Y
Y
Y
Y
Mouse
Y
Y
Y
Y
Y
Rat
Y
Y
Y
Y
Y
Rhesus macaque
No
Y
Y
Y
Y
Drosophila
No
Q2 2012
Q2 2012
Y
Y
Dog
No
Y
Y
Y
H2 2012
Pig
No
Y
Q2 2012
Y
H2 2012
Chicken
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Cow
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Zebrafish
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Horse
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Arabidopsis
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
Chinese Hamster
No
Q2 2012
Q2 2012
Q2 2012
H2 2012
For Internal Use Only
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Sample & Assay Technologies
14. Wet-Bench Validation of ALL qPCR Assays
• Sensitivity
Constant C(t) value for same amount of template
• Amplification Efficiency
DART-PCR analysis
• Specificity
• Single, symmetric dissociation curves
• Single band of appropriate size on agarose gel
• Dynamic Range
Linear over 8 logs of template
• NTC
No primer dimer formation
For Internal Use Only
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Sample & Assay Technologies
15. Exceptional Specificity
• Assays on Human TGFβ &
BMP Signaling Pathway
PCR Array used to analyze
BMP genes in Universal
Reference RNA.
• Single peak dissociation
curves
• Single gel bands of
predicted size
• High specificity for genes
difficult to design specific
primers for.
CONCLUSION: Each well on PCR Arrays detects a single gene-specific product.
For Internal Use Only
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Sample & Assay Technologies
16. Excellent Reproducibility
Reproducibility Among Different Users
Reproducibility Among Different Instruments
Human Drug Metabolism PCR Array in Universal Reference RNA
CONCLUSION: The PCR Arrays are SO reproducible that the same raw threshold cycle
data can be obtained for the same samples even from different end users at different
times or using different instruments.
For Internal Use Only
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Sample & Assay Technologies
19. Summary: PCR Arrays
Complete System for mRNA or miRNA Studies
- Four-component system: sample prep, arrays, master mix, first strand
kit, and free data analysis software
- Four-hour protocol from RNA to presentation-quality results
Breadth of Pathway Content
- More than 100 pathways: human, mouse, rat, monkey, dog
- FULLY CUSTOMIZABLE by gene, set, or pathway
VERY RELIABLE Real-Time PCR Performance
- Wet-bench validation of EVERY primer assay pre-sale
- Melt curve analysis to confirm single amplicon specificity
Hundreds of Peer-Reviewed Articles Using PCR Arrays
http://www.sabiosciences.com/support_publication.php
For Internal Use Only
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Sample & Assay Technologies
20. Presentation Overview
o QIAGEN’s SABiosciences portfolio
o What is a PCR Array and how do I use it?
o Cignal & Cignal Lenti Pathway Reporters
o Summary
For Internal Use Only
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Sample & Assay Technologies
21. Cignal Reporter Assays (45 Pathways)
Pathway
Amino Acid Deprivation
Androgen
Antioxidant Response
ATF6
C/EBP
cAMP/PKA
Cell Cycle
DNA Damage
EGR1
ER Stress
Estrogen
GATA
Glucocorticoid
Heat Shock Response
Heavy Metal Stress
Hedgehog
HNF4
Hypoxia
Interferon Regulation
Type I Interferon
Interferon Gamma
KLF4
Liver X
For Internal Use Only
Pathway
MAPK/ERK
MAPK/JNK
MEF2
c-myc
Nanog
NFkB
Notch
Oct4
Pax6
PI3K/AKT
PKC/Ca++
PPAR
Progesterone
Retinoic Acid
Retinoid X
Sox2
SP1
STAT3
TGF-beta
VDRE
Wnt
Xenobiotic
Transcription Factor
ATF4/ATF3/ATF2
Androgen Receptor
Nrf2 & Nrf1
ATF6
C/EBP
CREB
E2F/DP1
p53
EGR1
CBF/NF-Y/YY1
ER
GATA
GR
HSF
MTF1
Gli
HNF4
HIF-1
IRF-1
STAT1/STAT2
STAT1/STAT1
KLF4
LXR
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Transcription Factor
Elk-1/SRF
AP-1
MEF2
Myc/Max
Nanog
NFkB
RBP-Jk
Oct4
Pax6
FOXO
NFAT
PPAR
PR
RAR
RXR
Sox2
SP1
STAT3
SMAD2/3/4
Vitamin D Receptor
TCF/LEF
AhR
Sample & Assay Technologies
22. Cignal Reporter Assays: Experimental Design
For Internal Use Only
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Sample & Assay Technologies
28. Complimentary Arrays: Signal Transduction
•Signal Transduction Pathway Finder
•NFkB Signaling Pathway
•NFkB Signaling Targets
•TGFb Signaling Pathway
•TGFb Signaling Targets
•WNT Signaling Pathway
•WNT Signaling Targets
•Notch Signaling Pathway
•Notch Signaling Targets
For Internal Use Only
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Sample & Assay Technologies
29. Cignal Reporters: Benefits & Challenges
Breadth of Pathways and Research Applications
- 45 Pathway-Focused Reporter Assays
- 4 Application-Specific Cignal Finder 10-Pathway Arrays
Convenience
- Ready-to-use, validated, preformatted transient assays
Dual Modalities
- Dual-luciferase quantitative endpoint assays
- GFP dynamic live cell assays with single cell resolution
Biggest Unmet Need for Cignal Researchers
How do I use the Cignal Reporters in cells that
are difficult or impossible to transfect?
For Internal Use Only
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Sample & Assay Technologies
30. Cignal Pathway Reporter System Products
Primary cells, stem cells,
and difficult to transfect cell lines
Easy to
transfect cell lines
Endpoint
Assays
Cignal Dual-Luciferase
Reporter Assays
Single Pathway
Assays
For Internal Use Only
10-Pathway
Arrays
Dynamic
Live Cell Assays
Dynamic
Live Cell Assays
Endpoint
Assays
Cignal GFP
Reporter Assays
Cignal Lenti
Luciferase Reporters
Single Pathway
Assays
Single Pathway
Assays
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10-Pathway
Arrays
Cignal Lenti
GFP Reporters
Single Pathway
Assays
Sample & Assay Technologies
31. Cignal Lenti Reporter Assays (35 Pathways)
Pathway
Amino Acid Deprivation
Androgen
Antioxidant Response
ATF6
C/EBP
cAMP/PKA
Cell Cycle
DNA Damage
EGR1
ER Stress
Estrogen
GATA
Glucocorticoid
Heat Shock Response
Heavy Metal Stress
Hedgehog
HNF4
Hypoxia
Interferon Regulation
Type I Interferon
Interferon Gamma
KLF4
Liver X
For Internal Use Only
Pathway
MAPK/ERK
MAPK/JNK
MEF2
c-myc
Nanog
NFkB
Notch
Oct4
Pax6
PI3K/AKT
PKC/Ca++
PPAR
Progesterone
Retinoic Acid
Retinoid X
Sox2
SP1
STAT3
TGFβ
VDRE
Wnt
Xenobiotic
Transcription Factor
ATF4/ATF3/ATF2
Androgen Receptor
Nrf2 & Nrf1
ATF6
C/EBP
CREB
E2F/DP1
p53
EGR1
CBF/NF-Y/YY1
ER
GATA
GR
HSF
MTF1
Gli
HNF4
HIF-1
IRF-1
STAT1/STAT2
STAT1/STAT1
KLF4
LXR
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Transcription Factor
Elk-1/SRF
AP-1
MEF2
Myc/Max
Nanog
NFkB
RBP-Jk
Oct4
Pax6
FOXO
NFAT
PPAR
PR
RAR
RXR
Sox2
SP1
STAT3
SMAD2/3/4
Vitamin D Receptor
TCF/LEF
AhR
Sample & Assay Technologies
32. Cignal Lenti Reporters: Benefits
Transduce any mammalian cell
– Primary cells
– Stem cells
– Difficult-to-transfect cell lines
Transduction-ready
– No lentiviral generation
– No titering assays
Versatile System
– Transient experiments
– Generate pathway sensor cell
lines
For Internal Use Only
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Sample & Assay Technologies
34. NFkB Pathway Sensor Cell Line
Lenti Reporters Enable Rapid Pathway Sensor Cell Line Generation
For Internal Use Only
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Sample & Assay Technologies
35. Summary: Cignal Lenti Reporters
.
Breadth of Pathways and Arrays
• 35 Pathway-Focused Reporters
• 2 application-focused Cignal Finder Lenti 10-Pathway Arrays
.
Performance
Exceptional sensitivity, specificity, signal-to-noise ratio, and
reproducibility, using either luciferase or GFP reporter formats
.
High Efficiency Lentiviral Delivery System
• Study cell signaling in primary cells, stem cells, and difficult to
transfect cell lines
• Rapidly generate pathway sensor cell lines
.
Convenience
• Ready-to-use, validated reporters
• Don’t have to produce or amplify lentivirus in your laboratory
For Internal Use Only
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Sample & Assay Technologies
36. Take Home Message
Tell a better Biological Story from your experiments
• Publish faster and in higher impact journals
• Work SMARTER, NOT Harder
• Improve Success Rates of Your Grant Applications
• Expedite Drug Pipeline
For Internal Use Only
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Sample & Assay Technologies