RT2 Profiler PCR Arrays allow researchers to analyze gene expression in biological pathways or disease states using real-time PCR. The document discusses: 1. PCR Arrays focus on profiling genes relevant to specific pathways or disease states. They provide a simple, reproducible, and sensitive way to simultaneously profile expression of many genes related to a pathway. 2. Examples are provided demonstrating how PCR Arrays have been used in cancer research to discover breast cancer biomarkers, in immunology research to monitor cytokine induction, and in toxicity research to determine drug toxicity profiles. 3. Key advantages of PCR Arrays are highlighted, including their simplicity, performance, relevance to specific pathways, and ability to analyze gene expression from small amounts

1. PCR ARRAYS
RT2 ProfilerTM PCR ARRAYS
Apoptosis
Cancer
Cell Adhesion
Cell Signaling
Cytokines
Disease
Inflammation
Neuroscience
Stem Cells
Toxicology
Focus on your Pathway

2. PCR ARRAYS: Pathway Analysis with Real-Time PCR
How PCR ARRAYS Work
Focus on Your Pathway
What are PCR Arrays?
RT² Profiler PCR Arrays are the most reliable and sensitive gene
expression profiling technology for analyzing a focused panel of
genes in signal transduction, biological process, or disease related
pathways using real-time PCR.
How are PCR Arrays Utilized?
The RT² Profiler PCR Arrays have been increasingly used in
research on cancer, immunology, stem cells, toxicology, biomarker
discovery and validation, and phenotypic analysis of cells and
transgenic animals.
1. Convert Total RNA to cDNA.
cDNA 1
cDNA 2
2. Add cDNA to RT2 qPCR Master Mix & Aliquot Mixture Across
PCR Array.
Why PCR Arrays?
Simplicity
1.E-000
1.E-000
Delta Rn
1.E+001
1.E-001
1.E-003
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40
10-6
1.E-01
10-4
1.E-02
10-3
10-2
CCL8
CCR1
CCR2
CCR8
CCR9 CEBPB
CCR3
CCR4
CCR5
CCR6
CCR7
CCL5
CCL7
CRP
CX3CR1 CXCL1 CXCL10 CXCL11 CXCL12 CXCL13 CXCL14 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9
ICEBERG IFNA2
IL10
IL10RA IL10RB
IL13 IL13RA1 IL17C
IL1A
IL1B
IL1F10
IL1F5
IL8
IL8RA
IL8RB
IL1F6
IL1F7
IL1F8
IL1F9
IL1R1
IL1RN
IL22
IL5
IL5RA
IL9
IL9R
LTA
LTB
LTB4R
MIF
SCYE1
SPP1
TNF
HGDC
RTC
RTC
RTC
B2M
HPRT1 RPL13A GAPDH ACTB
HOUSEKEEPING
GENE CONTROLS
GENOMIC REVERSE TRANSCRIPTION
CONTROLS
DNA CONTROL
TNFSF5 TOLLIP XCR1
PPC
PPC
PPC
POSITIVE
PCR CONTROLS
4
Breast Tumor
Complete Systems Available
RT² First Strand Kit: cDNA Synthesis
Eliminates Genomic DNA
Insures RT Efficiency & Consistency
20-Minute Protocol: Quick & Simple
SYBR Green qPCR Master Mixes
Specific Amplification - No Primer Dimers
Maximum Amplification Efficiencies
Formulated for the Instrument in Your Lab
Data Analysis: Convert Raw Ct Data to Fold-Change Results
Easy-to-Use Web Portal
http://www.SABiosciences.com/pcrarraydataanalysis.php
Each well in a PCR Array represents the expression of a gene
related to a pathway or disease state. RTC Controls require the
use of the RT2 First Strand Kit.
www.SABiosciences.com
1.E-06
D
3
1.E+00
CCL4
CCL11 CCL13 CCL15 CCL16 CCL17 CCL18
-2
-1
0
1
2
Fold Change Ratio (log2)
TIMP3
1.E-01
CCL3
CCL1
C
-3
MMP9
ITGA2
MCAM
ITGB4
1.E-02
CCL20 CCL21 CCL23 CCL24 CCL25 CCL26
C5
1.E-04
ITGB3
1.E-03
CCL2
C4A
TGFB1
1.E-03
1.E-05
10-1
-4
CCNE1
CDKN2A
FGFR2
1.E-04
CCL19
C3
1.E+00
A
B
A
10-5
1.E-05
BCL6
Cycle Number
1.E-06
ABCF1
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40
4. Data Analysis.
D
Human Inflammatory Cytokines & Receptors RT2 Profiler PCR Array
1.E-003
Cycle Number
1
Anatomy of a PCR ARRAY
1.E-001
1.E-002
1.E-002
Normal Breast
Relevance
PCR Arrays focus on profiling the genes relevant to the
pathways or disease states of your interest.
Profile 2
Profile 1
1.E+001
Delta Rn
Performance
The PCR Arrays have the sensitive, reproducible, specific,
and reliable peformance to accurately profile multiple genes
simultaneously in 96- or 384-well formats.
3. Run in Your Real-Time PCR Instrument.
p-Value for Fold Change
The simplicity of the PCR Arrays makes expression profiling
accessible for routine use in every research laboratory with
a real-time PCR instrument.
Support@SABiosciences.com

3. PCR ARRAYS: Performance
Reproducibility
Sensitivity
100
High Reproducibility Among Different Users
Use as little as 25 ng Total RNA
B1
40
B2
40
B3
40
A1
20
20
20
20
10
10
10
0
0
0
10
20
30
40 0
40
10
20
30
40 0
40
10
20
30
0
40 0
40
30
20
500
1000
100
Input RNA [ng]
50
30
20
20
20
10
0
40
0
10
20
30
40 0
40
10
20
30
40 0
40
10
20
30
0
40 0
40
30
30
20
20
20
10
0
0
40
0
10
20
30
40 0
40
10
20
30
40 0
40
10
20
30
0
40 0
40
30
A4
30
30
20
20
20
40
20
Signal [-d(RFU)/dT]
0
110
90
70
50
30
10
-10
110
90
70
50
30
10
-10
110
90
70
50
30
10
-10
70
60
80
90
BMP3
9.8
08
70
60
BMP5
70
60
80
80
BMP7
60
90
8.8
22
90
8.
72
70
BMP1
80
BMP2
90
BMP3
130
110
90
70
50
30
10
-10
110
90
70
50
30
10
-10
130
110
90
70
50
30
10
-10
110
90
70
50
30
10
-10
10
30
40
10
20
30
40
10
0
10
20
30
40
0
0
10
20
30
40
0
0
10
20
30
40
0
0
PCR Arrays Yield Highly Reproducible Results
Four replicate sets of raw threshold data (1-4) obtained by two
different scientists (A & B) at two different times on Human Drug
Metabolism RT2 Profiler PCR Arrays
Correlation Coefficients
are directly compared. The results
A4
A2
A3
A1
R2
demonstrate a high degree of corB1 0.993 0.989 0.995 0.992
2
relation (R > 0.990).
0.992
80
70
60
Accuracy
8.8
97
BMP2
BMP4
90
8.5
43
120
Uniformly High PCR Amplification Efficiency
100
80
70
60
80
70
60
90
8.7
38
BMP6
90
BMP15
8.7
61
80
70
60
Tm [Co]
BMP4
20
Ct from User B
Amplification Efficiency [%]
8.
86
10
20
10
Single Dissociation Curves
BMP1
40
B2 0.994 0.990 0.995
B3 0.992 0.990 0.993 0.992
B4 0.993 0.992 0.994 0.992
Specificity
80
30
30
0
60
20
10
0
10
100
10
20
10
25
PCR Arrays Let You See More Genes with Less RNA
Different amounts of universal total RNA were characterized
using the Human Inflammatory Cytokines and Receptors PCR
Array, and the percentage of detectable genes was calculated for each RNA amount.
As little as 25 ng total RNA yields greater than an 80% positive
call, even for cytokines expressed at very low levels.
40
30
10
A3
30
Human Inflammatory Cytokines & Receptors PCR Array
30
10
0
20
20
10
10
30
0
A2
30
10
Ct from User A
% Positive Calls
30
40
40
0
30
0
60
30
10
80
B4
40
30
BMP5
BMP6
BMP7
90
BMP15
Agarose Gel
PCR Arrays Amplify A Single Gene-Specific Product in Every Reaction
Universal total RNA was characterized on the TGFβ / BMP Signaling
Pathway PCR Array, followed by dissociation (melt) curve analysis.
PCR Arrays specifically detect individual genes despite the expression
of related gene family members in the same RNA sample.
80
60
40
20
0
Gene
PCR Arrays Yield the Most Accurate Results
A representative set of assays for 4,000 genes used in RT2 PCR
Arrays have an average amplification efficiency of 99% with a
95% confidence interval from 90-110%.
Consistently high amplification efficiencies enable PCR
Arrays to accurately analyze multiple genes simultaneously
utilizing the ΔΔCt method.

4. PCR ARRAYS: Application Examples
Cancer Research: ECM PCR ARRAYS for Breast Cancer Biomarker Discovery
ECM & Cell Adhesion
101
UP
-R
EG
UL
AT
ED
Breast Tumor
100
10-1
C L A
O 4 2
C N D
T N 2
S L
E E
10-2
A A T 1
D M S
I G 4
T B
M P
M 9
T M 3
I P
10-3
M P
M 3
10-5
C T 1
N N
F 1
N
DO
WN
-R
EG
UL
AT
ED
I G 3
T B
10-4
Extracellular Matrix &
Adhesion Signaling Pathway
ECM & Cell Adhesion PCR Arrays Revealed
Up- & Down-Regulated Genes in Breast Cancer
Total RNA from normal human breast and a
human breast tumor were characterized in
technical triplicates, and the relative expression
levels for each gene in the two samples are
plotted against each other in the Scatter Plot.
Genes encoding the matrix metallopeptidases
(MMP3 & MMP9) and their inhibitors (TIMP3) are
up-regulated, while genes encoding integrins
(ITGB3 & ITGB4) are down-regulated, by at least
three-fold (outside the silver field) in breast
tumors relative to normal tissue.
NO
10-5
GE
AN
CH
10-3
10-4
10-2
101
100
10-1
Normal Breast
Immunology Research: Monitoring Cytokine Induction with PCR ARRAYS
Common Cytokines
10-9
10-8
I 9
L
10
-7
C F
S 2
I 1
L 0
I 1
L A
T F
N
I 1
L B
10-6
p value
S A I T C L S G I I A C
T T S I A
I N F C N E
Common Cytokine PCR Array Identified 23 Up-Regulated
and 6 Down-Regulated Genes Following PMA and
Ionomycin Treatment
Triplicate total RNA samples from human peripheral
blood mononuclear cells (either untreated or stimulated
with 50 ng/mL PMA and 1 µg/mL ionomycin for 6 hours)
were characterized.
Twenty-three cytokine genes are up-regulated (> 5-fold,
p < 0.0005) including interleukins, colony stimulating
factors, and TNF ligands after 6 hours of stimulation. Six
interleukin and TNF ligand genes are down-regulated
under the same conditions.
T F F 0
N S 1
L A
T
10
I 1
L 1
C F
S 1
I 5
L
-5
P G A
D F
T F 2
G B
10-4
I 2
L 1
I 2
L 2
I 1
L 3
I 3
L
I 1
L 7
T F F 1
N S 1
T F F 3
N S 1 B
B P
M 6
I N 5
F A
10-3
I 2
L
I N
F G
T F S S 1 B
N R P F 1
T F F 4
N S 1
B P
M 3
I 1 7
L F
10-2
10-1
10 0
-7 -5 -3 -1
1 3 5 7 9 11 13 15 17
fold difference [log2]
Common Cytokines Network
Toxicity Research: Determining Drug Toxicity with PCR ARRAYS
128
FAX:
119
30
20
888.465.9859
INTERNATIONAL TEL:
HSPA6
CRYAB
CSF2
MT2A
HSPA1A
TNF
DDIT3
HSPH1
CYP1A1
HSPA5
HSPCA
DNAJB4
HMOx1
10
1GADD45A
DNA Repair
Mechanism Pathway
888.503.3187
5005
Actos
Avandia
Rezulin
125
0
USA TEL:
Stress & Toxicity PathwayFindertm
18SrRNA
1ACTB
Fold Up-Regulation
5000
Stress & Toxicity PathwayFinder PCR Array
Uncovered Distinct Gene Expression Profiles
Associated with Liver Toxicity Caused by 3
PPARγ Agonists
RNA from HepG2 cells treated with three different
glitazone PPARγ agonists for type 2 diabetes
mellitus was characterized, and the results were
compared to that of a vehicle (DMSO) control.
A withdrawn drug with idiosyncratic liver toxicity
(Rezulin) induces very different changes in the
expression of stress-related genes than two safer
drugs still on the market (Avandia and Actos).
+1 301.682.9200
FAX:
+1 301.682.7300

5. What’s Your Pathway?
Pathway / Topic Focus
Alzheimer’s Disease
Angiogenesis
Angiogenic Growth Factors & Angiogenesis Inhibitors
Apoptosis
Breast Cancer and Estrogen Receptor Signaling
Cancer Drug Resistance and Metabolism
Cancer miRNA
Cancer PathwayFinder
Cell Cycle
Chemokines and Receptors
Common Cytokines
DNA Damage Signaling Pathway
Drug Metabolism
Drug Transporters
EGF / PDGF Signaling Pathway
Extracellular Matrix and Adhesion Molecules
Growth Factors
Heat Shock Proteins
HIV Infection & Host Response
Hypoxia Signaling Pathway
Inflammatory Cytokines and Receptors
Inflammatory Response & Autoimmunity
Innate & Adaptive Immune Responses
Interferons (IFN) and Receptors
JAK / STAT Signaling Pathway
MAP Kinase Signaling Pathway
Neurogenesis & Neural Stem Cells
Neuroscience Ion Channels and Transporters
Neurotransmitter Receptors and Regulators
Neurotrophins and Receptors
NF B Signaling Pathway
Nitric Oxide Signaling Pathway
Notch Signaling Pathway
Osteogenesis
Oxidative Stress and Antioxidant Defense
p53 Signaling Pathway
PI3K / AKT Signaling Pathway
Signal Transduction PathwayFinder
Stem Cell
Stress and Toxicity PathwayFinder
TGFβ / BMP Signaling Pathway
Th17 for Autoimmunity and Inflammation
Th1-Th2-Th3
Toll-Like Receptor Signaling Pathway
Tumor Metastasis
Tumor Necrosis Factor (TNF) Ligands and Receptors
Wnt Signaling Pathway
Custom PCR Arrays
PCR Array Gene Expression Analysis Service
Which RealTime PCR Instrument?
PCR ARRAY Catalog #
Rat
Human Mouse
PAHS-057
PAHS-024
PAHS-072
PAHS-012
PAHS-005
PAHS-004
MAH-102
PAHS-033
PAHS-020
PAHS-022
PAHS-021
PAHS-029
PAHS-002
PAHS-070
PAHS-040
PAHS-013
PAHS-041
PAHS-076
PAHS-051
PAHS-032
PAHS-011
PAHS-077
PAHS-052
PAHS-064
PAHS-039
PAHS-061
PAHS-404
PAHS-036
PAHS-060
PAHS-031
PAHS-025
PAHS-062
PAHS-059
PAHS-026
PAHS-065
PAHS-027
PAHS-058
PAHS-014
PAHS-405
PAHS-003
PAHS-035
PAHS-073
PAHS-034
PAHS-018
PAHS-028
PAHS-063
PAHS-043
Inquire
Inquire
PAMM-057
PAMM-024
PAMM-072
PAMM-012
PAMM-005
PAMM-004
MAM-102
PAMM-033
PAMM-020
PAMM-022
PAMM-021
PAMM-029
PAMM-002
PAMM-070
PAMM-040
PAMM-013
PAMM-041
PAMM-076
PAMM-051
PAMM-032
PAMM-011
PAMM-077
PAMM-052
PAMM-064
PAMM-039
PAMM-061
PAMM-404
PAMM-036
PAMM-060
PAMM-031
PAMM-025
PAMM-062
PAMM-059
PAMM-026
PAMM-065
PAMM-027
PAMM-058
PAMM-014
PAMM-405
PAMM-003
PAMM-035
PAMM-073
PAMM-034
PAMM-018
PAMM-028
PAMM-063
PAMM-043
Inquire
Inquire
PARN-057
PARN-024
PARN-072
PARN-012
PARN-005
PARN-004
PARN-033
PARN-020
PARN-022
PARN-021
PARN-029
PARN-002
PARN-070
PARN-040
PARN-013
PARN-041
PARN-076
PARN-051
PARN-032
PARN-011
PARN-077
PARN-052
PARN-064
PARN-039
PARN-061
PARN-404
PARN-036
PARN-060
PARN-031
PARN-025
PARN-062
PARN-059
PARN-026
PARN-065
PARN-027
PARN-058
PARN-014
PARN-405
PARN-003
PARN-035
PARN-073
PARN-034
PARN-018
PARN-028
PARN-063
PARN-043
Inquire
Inquire
Supported PCR Instruments
Applied Biosystems (ABI)
7000, 7300, 7500, 7500 FAST, 7700, 7900HT,
StepOnePlus (96- & 384-well blocks)
Bio-Rad
iCycler, iQ5, MyiQ, Chromo4, Opticon, Opticon 2
Stratagene
Mx3000P, Mx3005P, Mx4000
Roche
LightCycler 480 (96- & 384-well bocks)
Eppendorf
Mastercycler ep realplex
Complete the PCR ARRAY System
Product
Pack Size
Price
The RT2 First Strand Kit is required for use with PCR Arrays.
RT2 First
Strand Kit
12 Arrays
$ 199
PCR Array pack sizes of 12 & 24 offer the best value.
PCR Arrays
2 Arrays (96-well)
12 Arrays (96-well)
24 Arrays (96-well)
4 Arrays (384-well)
$ 499
$ 1599
$ 2499
$ 999
RT2 SYBR Green qPCR Master Mixes are necessary for use
with PCR Arrays. The Master Mix is available with ROX,
Fluorescein, or SYBR Green only.
Master
Mix
2 Arrays
12 Arrays
24 Arrays
$ 189
$ 999
$ 1599
Guaranteed Performance
Over 100 Pathways Available
Focus on your Pathway

6. Angiogenesis
Disease
Apoptosis
Inflammation
Cancer
Neuroscience
Cell Signaling
Stem Cells
Cytokines
Toxicology
(Formerly SuperArray Bioscience Corporation)
6951 Executive Way, Frederick, MD 21703 USA
Phone: 301.682.9200
www.SABiosciences.com
The PCR Array Experts
100+ Pathways Available
Guaranteed Peformance
Fax: 301.682.7300
support@SABiosciences.com
©2009 SABiosciences Corporation All Rights Reserved.
RT2 Profiler PCR Array, RT2 Real-Time, PathwayFinder, Focus on Your Pathway, Pathways, SABiosciences & the SA logo are trademarks of SABiosciences Corporation.
SYBR is a registered trademark of Molecular Probes, Inc. Actos is a registered trademark of Takeda Pharmaceutical Company, Ltd. Avandia is a registered trademark
of GlaxoSmithKline. Rezulin is a registered trademark of Parke-Davis Pharmaceuticals, Ltd. ABI and StepOnePlus are registered trademarks of Applera Corporation.
Opticon, Chromo4, iQ5, iCycler and MyiQ are registered trademarks of Bio-Rad Laboratories. Mx3000P, Mx3005P, and Mx4000 are registered trademarks of Stratagene.
LightCycler is a registered trademark of Roche Molecular Systems. Mastercycler is a registered trademark of Eppendorf, Inc.