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Rt2 profilerbrochure

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  • 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.