Brochure PCR Array - Pathway ( /2011)

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1 RT 2 Profiler PCR Arrays Focus on Your PCR Sample & Assay Technologies

2 Table of contents RT 2 Profiler PCR Arrays 3 RT 2 Profiler PCR Array 5 RT 2 Profiler PCR Array 8 FFPE RT 2 PreAMP 9 RT 2 Profiler PCR Array 1 QIAGEN RNeasy Kits 11 QIAGEN 12 RNA QIAGEN 13 RT 2 Profiler PCR Array 14 PCR QIAGEN Rotor-Gene Q Rotor-Gene 6 R Applied Biosystems ABI Bio-Rad Stratagene Roche ABI ABI 75 Standard ViiA 7 96-well block ABI 75 FAST ViiA 7 FAST 96-well Block ABI 79HT Standard 96-well Block77 ABI 79HT FAST 96-well Block ABI 79HT ViiA well Block ABI StepOnePlus icycler iq5 MyiQ MyiQ2 Chromo4 CFX96 Opticon 2 CFX384 Mx3P Mx35P Mx4 LightCycler well Block LightCycler well Block Eppendorf Mastercycler ep realplex 2/2S 4/4S A TaKaRa TP-8 A Fluidigm BioMark H RT 2 Profiler PCR Array RT 2 Profiler PCR Arrays RT 2 SYBR Green ROX qpcr Mastermix RT 2 SYBR Green Fluor qpcr Mastermix RT 2 SYBR Green qpcr Mastermix 2 arrays 96-well 12 arrays 96-well 24 arrays 96-well 4 arrays 384-well 2 arrays 96-well 12 arrays 96-well 24 arrays 96-well 4 arrays 384-well 2 arrays 96-well 12 arrays 96-well 24 arrays 96-well 4 arrays 384-well A A C A C E C A D E A D F G Cat. no. RT 2 First Strand Kit 12 samples 3341 Cat. no RT 2 Profiler PCR Arrays Angiogenesis Apoptosis Autophagy Breast Cancer and Estrogen Receptor Signaling Cancer Finder Cell Cycle Chemokines and Receptors Diabetes DNA Damage Signaling Drug Metabolism EGF/PDGF Signaling Embryonic Stem Cells Endothelial Cell Biology Epigenetic Chromatin Modification Enzymes Epithelial to Mesenchymal Transition Extracellular Matrix and Adhesion Molecules GPCR Signaling Growth Factors Heat Shock Proteins Hedgehog Signaling Hematopoietic Stem Cells & Hematopoesis Hepatoxicity Hypoxia Signaling Inflammatory Cytokines and Receptors Innate and Adaptive Immune Response Interferon α,β Response JAK/STAT Signaling MAP Kinase Signaling Mitochondrial Energy Metabolism Nephrotoxicity NFkB Signaling Oxidative Stress and Antioxidant Defense p53 Signaling WNT Signaling * XX = Y = PCR Array Cat. no.* PAXX-24Y PAXX-12Y PAXX-84Y PAXX-5Y PAXX-33Y PAXX-2Y PAXX-22Y PAXX-23Y PAXX-29Y PAXX-2Y PAXX-4Y PAXX-81Y PAXX-15Y PAXX-85Y PAXX-9Y PAXX-13Y PAXX-71Y PAXX-41Y PAXX-76Y PAXX-78Y PAXX-54Y PAXX-93Y PAXX-32Y PAXX-11Y PAXX-52Y PAXX-16Y PAXX-39Y PAXX-61Y PAXX-8Y PAXX-94Y PAXX-25Y PAXX-65Y PAXX-27Y PAXX-43Y 2 RT 2 Profiler PCR Arrays Analysis 3/211

3 RT 2 Profiler PCR Arrays RT 2 Profiler PCR Array RT 2 RT Profiler PCR Array PCR RT 2 Profiler PCR Array 5 DNA GDC cdna RTC PCR PPC RT 2 Profiler PCR Array RT 2 Profiler PCR Array RT 2 Profiler PCR Array 96/384 1-well disc 96 x 96 chip RT 2 Profiler PCR Array FFPE RNA RNA cdna RT 2 Real Time PCR Reverce Transcription RT RT x RT = RT 2 RT square RT cdna RT 2 SYBR Green qpcr Mastermix RT 2 Profiler PCR Array RT 2 Profiler PCR Array plate layout PCR E+1 1.E Delta Rn 1.E- 1.E-1 1.E-2 Delta Rn 1.E- 1.E-1 1.E E-3 1.E Cycle Number Cycle number HK1 HK2 HK3 HK4 Housekeeping genes HK5 GDC Genomic DNA control RTC RTC RTC Reverse transcription controls PPC PPC PPC Positive PCR controls 1. RT 2 Profiler PCR Array well disc 96 x 96 chip p-value for fold change Breast tumor Fold change ratio log2 Normal breast RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 3

4 TaqMan log 2 FC R =.97 Slope = genes RT 2 PCR log 2 FC C T TaqMan E = 1% R 2 =.9998 SYBR Green E = 1% R 2 = Log [copy number] 2. * RT² Profiler PCR Arrays SYBR Green TaqMan POLR2A fold difference 2 3. RT 2 SYBR Green TaqMan * SYBR Green TaqMan TaqMan PCR SYBR Green C T TaqMan 4. Stress and Toxicity Finder RT² Profiler PCR Array 3 PPARγ II 3 PPARγ HepG2 RNA DMSO Rezulin 2 Avandia Actos Fold up-regulation Actos Avandia Rezulin HSPA6 CRYAB MT2A CSF2 HSPA1A DDIT3 TNF CYP1A1 HSPH1 HSPA5 HSPCA DNAJB4 1GADD45A HMOx1 1ACTB 18SrRNA 5. Common Cytokine RT 2 Profiler PCR Array PBMC ng/ml PMA 1 mg/ml 6 RNA Common Cytokine RT 2 Profiler PCR Array triplicate 6 TNF 23 5 p <.5 6 TNF p value IL1A IL1 IFNG CSF2 IL9 1 7 TNF TNFSF1 IL1B LTA IL CSF1 IL21 IL5 IL13 IL TNFSF13B TGFB2 PDGFA 1 4 TNFSF11 IL1F7 BMP6 TNFRSPSF11B IL IFNA5 TNFSF14 BMP3 IL2 IL Fold difference [log 2 ] 6. Anagiogenesis RT 2 Profiler PCR Array fold change IgG EGFR mab225 T4-2 RNA Angiogenesis RT 2 Profiler PCR Array 84 5 Fold change fold change SABiosciences Fold change mab 225/LgG IL8 PGF MMP9 NRP2 EREG THBS1 PECAM1 IL6 ENG PTGS1 MDK FGF2 VEGFC SPHK1 TGFB1 ACTB VEGFA IL1B TGFA TIMP1 LAMA5 ECGF1 CXCL1 TNFA B2M FGFR3 JAG1 SERPINF1 FIGF TIMP3 FGF1 ANGPT1 * Arikawa, E., et al. (28) Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics 9, 378. Chen, A., et al. (29) Endothelial cell migration and vascular endothelial growth factor expression are the result of loss of breast tissue polarity. Cancer Research 69, RT 2 Profiler PCR Arrays Analysis 3/211

5 RT 2 Profiler PCR Array RT 2 Profiler PCR Array RT 2 Profiler PCR Array RT 2 Profiler PCR Array 4 RT 2 Profiler PCR Array DNA gdna PCR RT 2 Profiler PCR Array RT 2 Profiler PCR Arrays RT 2 Profiler PCR Array 89 RT 2 qpcr Primer Assays RNA FFPE RNeasy Kits RT 2 SYBR Green qpcr Mastermixes RNA ROX Fluorescein RT 2 First Strand Kit RT 2 Profiler PCR Array RNA RNA DNA gdna mrna RT 2 Profiler PCR Array RT 2 Profiler PCR Array C T fold change DNA cdna Buffer GE RT enzyme Oligo-dTs Random hexamers External RNA control (RTC) dntps Hot-start DNA polymerase dntps SYBR Green dye DNA SYBR Green Resolution RT 2 SYBR Green qpcr Mastermix RT 2 First Strand Kit RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 5

6 A B C T GDC Untreated HEK293T cells GE treated Mouse spinal tissue Clean of gdna RNA source Mouse brain tissue Rat brain tissue Average C T (RTC-PPC) Fail Pass None Mg 2+ TRIzol Addition / treatment 7. A DNA HEK 293T RNA RT 2 First Strand Kit gdna Elimination Buffer RT 2 Profiler PCR Arrays B Human universal RNA RNA TRIzol RT 2 First Strand Kit cdna Gene layout examples Custom RT 2 Profiler PCR Array 96-well format 384-well format 12 genes - 8 samples/plate 16 genes - 24 sample/plate 24 genes - 4 samples/plate 32 genes - 12 sample/plate Custom RT 2 Profiler PCR Arrays Custom RT 2 Profiler PCR Array 384 Custom RT 2 Profiler PCR Array 32 genes - 3 samples/plate 48 genes - 2 samples/plate 96 genes - 1 sample/plate 48 genes - 8 samples/plate 96 genes - 4 sample/plate 384 genes - 1 sample/plate Custom RT 2 Profiler PCR Arrays Custom RT 2 Profiler PCR Array Custom RT 2 Profiler PCR Array 4 custom RT² Profiler PCR Array 6 RT 2 Profiler PCR Arrays Analysis 3/211

7 Fold change over WT MECP2-Tg MECP2-null Gene Activated Repressed 8. MECP2 qpcr 66 4 MECP2-Tg MECP2 4 MECP2-null MECP P <.5 t 1 4 * 96-well plate 1-well disc custom RT 2 Profiler PCR Arrays Custom RT 2 Profiler PCR Array Rotor-Gene Q format well disc format 384-well custom RT 2 Profiler PCR Arrays Modified RT 2 Profiler PCR Arrays RT 2 Profiler PCR Arrays 4 96-well 1-well disc RT 2 Profiler PCR Arrays well RT 2 Profiler PCR Array Cat. no. RT 2 PreAMP cdna Synthesis Kit RT 2 PreAMP Primer Mixes pathway focused 12 genes - 8 sample/plate 96 genes - 1 sample/plate * Chahrour, M., et al. (28) MeCP2, A key contributor to neurological disease, activates and represses transcription. Science 32, x 96 Fluidigm BioMark RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 7

8 RT 2 Profiler PCR Array Signal [-d(rfu/dt] CXCR1 CXCR2 CXCL2 CXCL T m [ C] 9. RT 2 Profiler PCR Array Universal total RNA 4 RT 2 qpcr Primer Assay RNA RT 2 Profiler PCR Arrays % positive call PreAMP Unamp Input RNA [ng] 1. RT 2 Profiler PCR Array 1 ng RNA Universal total RNA Human Inflammatory Cytokines and Receptors RT 2 Profiler PCR Array PAHS-11 RT 2 PreAMP 9 RNA PreAMP 1 ng RNA RT 2 Profiler PCR Arrays RT 2 qpcr Primer Assay RT² Profiler PCR Array RT 2 Profiler PCR Array RT 2 qpcr Primer Assay RT 2 Profiler PCR Array RNA 1 qpcr 2, RT 2 qpcr Primer Assays RT 2 Profiler PCR Array RT 2 Profiler PCR Array 25 ng 5 µg RNA 85 positive call RT 2 PreAMP 9 1 ng RNA >9 positive call PCR 8-log Fluorescence Cycle number 11. RT 2 Profiler PCR Arrays RNA CHRNA5 1 RT 2 qpcr Primer Assay 8 RT 2 Profiler PCR Arrays Analysis 3/211

9 FFPE RT 2 PreAMP FFPE FFPE qrt-pcr RT 2 PreAMP multiplex tandem PCR cdna FFPE RNA cdna RT 2 Profiler PCR Arrays RNA RNA RT 2 Profiler PCR Arrays FFPE FFPE RT 2 PreAMP RNeasy FFPE Mini Kit FFPE RNA RT 2 PreAMP FFPE qrt-pcr RT 2 PreAMP FFPE positive call rate cdna FFPE C T y =.9749x.589 R 2 = PreAMP C T 12. RT 2 PreAMP FFPE fold change FFPE RNA cdna 4 cdna Human Cancer Finder RT 2 Profiler PCR Array C T 33 C T Raw C T RT only RT + PreAMP CASP8 CDKN2A E2F1 FGFR2 IFNA1 MET MMP1 TERT TIMP3 TWIST1 ANGPT1 CDC25A JUN IFNB1 13. FFPE RNA RT 2 PreAMP RNA FFPE cdna RT 2 PreAMP PreAMP Human Cancer Finder RT² Profiler PCR Array C T C T 3 RT 2 PreAMP C T = 1 3 Cat. no. RT 2 PreAMP cdna Synthesis Kit RT 2 PreAMP Primer Mixes for all RT 2 Profiler PCR Arrays RT 2 PreAMP Primer Mixes for custom RT 2 Profiler PCR Arrays RT 2 Profiler PCR Arrays RT 2 SYBR Green qpcr Mastermixes Varies Varies RNeasy FFPE Kit (5) 7354 RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 9

10 RT 2 Profiler PCR Array RT² Profiler PCR Array RT² Profiler PCR Array C T C T foldchange fold-change replicate DNA positive PCR RT 2 Profiler PCR Array RT 2 Profiler PCR Array Data Analysis Suite * Excel png * Excel 1. Excel PCR Array Data Analysis Tutorial X log2 fold-difference Y replicate C T t p fold-differences 1 RT 2 Profiler PCR Arrays Analysis 3/211

11 QIAGEN RNeasy Kits RNeasy Kits RNeasy Kits RNA Agilent RIN RNA integrity number RNA RT-PCR RNeasy Kits RNA RNA RNA RNA RT-PCR RNeasy Kits RNeasy Kit RNase RNA RNA RNeasy RNeasy 96 plate RNA RNase RNA RNeasy A B RNA RFU 2 1 min 131. nt nt nt 5 min 1 min 15. RNA RNeasy Mini Kit Jurkat RNA RNA A QIAxcel system 28S 18S rrna 1.55 B Agilent 21 Bioanalyzer 28S 18S rrna RIN RNA FU Cat. no. RNeasy Mini Kit (5)* For purification of RNA from cells & easy-to-lyse tissues 7414 RNase-Free DNase Set (5) For DNase digestion RNA purification RNeasy Fibrous Tissue Mini Kit (5)* For purification of RNA from fiber-rich tissues 7474 RNeasy Plus Universal Mini Kit (5)* For purification of RNA from all tissue types 7344 RNeasy 96 Kit (12) For purification of RNA from cells in 96-well format QIAzol Lysis Reagent (2 ml) For lysis of fatty and standard tissues before RNA isolation 7936 * QIAcube RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 11

12 QIAGEN RNA RNA RNA RNA concentration [ng/μl] TissueLyser LT TissueLyser II Skin Heart Lung Brain 16. TissueLyser LT TissueLyser II RNeasy Fibrous Tissue MiniKit RNeasy Lipid Tissue Mini Kit QIAcube 2 mg RNA RNA 5 µl QIAGEN QIAGEN QIAshredder TissueRuptor TissueLyser TissueRuptor TissueLyser QIAGEN QIAshredder QIAshredder TissueRuptor TissueRuptor Disposable Probe TissueLyser TissueLyser LT 12 TissueLyser II Cat. no. QIAshredder (5) For homogenization of cell lysates TissueRuptor For disruption of individual samples TissueRuptor Disposable Probes (25) Disposable probes for use with the TissueRuptor 9989 TissueLyser LT For disruption of up to 12 samples 856 TissueLyser LT Adapter, 12-tube For purification of RNA from cells in 96-well format 6998 TissueLyser II For disruption of up to 48 or 192 samples 853 TissueLyser Adapter Set 2 x 24 Adaptor set for use with the TissueLyser II; holds 48 tubes RT 2 Profiler PCR Arrays Analysis 3/211

13 RNA QIAGEN RNA RNA RNA RNase mrna RNA RNA RNA QIAGEN RNA QIAGEN RNA RNA RNA QIAGEN A 1 Fold change in transcript level B Fold change in transcript level hrs 2 hrs Allprotect 4 hrs Allprotect 4 hrs PBS 24 hrs PBS 24 hrs 2 hrs 2 hrs 4 hrs 4 hrs 24 hrs 24 hrs 17. RNA Allprotect Reagent PBS RT-PCR A c-fos B Madh7 Allprotect Reagent Cat. no. Allprotect Tissue Reagent (1 ml) For stabilization of RNA, DNA, & protein in tissues 7645 AllPrep DNA/RNA Mini Kit (5) For simultaneous purification of DNA and RNA 824 RNAlater RNA Stabilization Reagent (25 ml) For stabilization of RNA in tissues 7616 RNeasy Protect Mini Kit (5) For stabilization of RNA in tissues and RNA purification RNAprotect Cell Reagent (25 ml) For stabilization of RNA in cells RNAprotect Animal Blood Tubes (5 x 1 µl) RNeasy Protect Animal Blood Kit (5) mirneasy Protect Animal Blood Kit (5) For collection of 1 µl animal blood with RNA stabilization For purification of RNA from blood collected in RNAprotect Animal Blood Tubes For purification of RNA, including mirna, from blood collected in RNAprotect Animal Blood Tubes QIAGEN Handbook User Manual QIAGEN Handbook User Manual RNAlater is a trademark of AMBION, Inc., Austin, Texas and is covered by various U.S. and foreign patents. Trademarks: QIAGEN, QIAcube, QIAxcel, QIAzol, AllPrep, RNAprotect, RNeasy, Rotor-Gene, TissueRuptor (QIAGEN Group); SYBR (Molecular Probes, Inc.); Roche, LightCycler, TaqMan (Roche Group); ABI, Applied Biosystems, ROX, ViiA, StepOnePlus (Applera Corporation or its subsidiaries); Eppendorf, Mastercycler (Eppendorf AG); Stratagene (Stratagene); Bio-Rad (Bio-Rad Laboratories, Inc.); Fluidigm (Fluidigm Corp.); Agilent (Agilent Technologies, Inc.); Excel (Microsoft Corporation); Actos (Takeda Pharmaceutical Company Limited); Avandia (GlaxoSmithKline); Rezulin (Parke-Davis Pharmaceuticals, Ltd.). 211 QIAGEN, all rights reserved. RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 13

14 RT 2 Profiler PCR Array RT 2 Profiler PCR Array 2 Apoptosis Alzheimer's Disease Angiogenesis Apoptosis Autophagy Angiogenesis Apoptosis Autophagy Cancer Finder Breast Cancer and Estrogen Receptor Signaling Breast Cancer and Estrogen Receptor Signaling Cancer Finder Cell Cycle Cancer Finder Cancer Drug Resistance and Metabolism Cell Cycle DNA Damage Signaling Cell Surface Markers Cancer Finder DNA Damage Signaling DNA Repair Dendritic and Antigen Presenting Cell Cell Cycle DNA Repair Endothelial Cell Biology Epigenetic Chromatin Modification Enzymes DNA Damage Signaling Epithelial to senchymal Transition (EMT) Heat Shock Proteins Epigenetic Chromatin Remodeling Factors EGF/PDGF Signaling MAP Kinase Signaling NFκB Signaling Epithelial to esenchymal Transition (EMT) Epithelial to Mesenchymal Transition (EMT) mtor Signaling Oxidative Stress and Antioxidant Defense Extracellular Matrix and Adhesion Molecules MAP Kinase Signaling Neurogenesis and Neural Stem Cell p53 Signaling Glucose Metabolism p53 Signaling NFκB Signaling PI3K-AKT Signaling Hematopoietic Stem Cells and Hematopoiesis PI3K-AKT Signaling p53 Signaling Stress and Toxicity Finder Homeobox (HOX) Genes Protein Phosphatases PI3K-AKT Signaling TNF Ligand and Receptor Mesenchymal Stem Cell TGFβ BMP Signaling Protein Phosphatases Tumor Suppressor Genes Stem Cell Tumor Metastasis Signal Transduction Finder Ubiquitination T-cell and B-cell Activation Tumor Suppressor Genes Transcription Factors Unfolded Protein Response Th1-Th2-Th3 WNT Signaling Ubiquitination RT 2 Profiler PCR Array RT 2 Profiler PCR Arrays Analysis 3/211

15 Chemokines & Receptors Angiogenic Growth Factors & Angiogenesis Inhibitors Alzheimer's Disease camp/ca 2+ Signaling Finder Adipogenesis Cancer Drug Resistance and Metabolism Common Cytokine Atherosclerosis Apoptosis EGF/PDGF Signaling Dendritic and Antigen Presenting Cell Cancer Finder Inflammasomes Chemokines and Receptors Autophagy G Protein Coupled Receptors Embryonic Stem Cells Cardiotoxicity Inflammatory Cytokines and Receptors Common Cytokine Drug Transporters GPCR Signaling Finder Hedgehog Signaling Cell Cycle Inflammatory Response and Autoimmunity Embryonic Stem Cells Embryonic Stem Cells Heat Shock Proteins Hematopoietic Stem Cells and Hematopoiesis DNA Damage Signaling Interferon α, β Response Endothelial Cell Biology GPCR Signaling Finder Hedgehog Signaling Homeobox (HOX) Genes Drug Metabolism Interferon and Receptor Extracellular Matrix and Adhesion Molecules Heat Shock Proteins Insulin Signaling Lipoprotein Signaling and Cholesterol Metabolism Drug Metabolism: Phase I Enzymes JAK/STAT Signaling Glycosylation Hedgehog Signaling JAK/STAT Signaling Mesenchymal Stem Cell Drug Metabolism: Phase II Enzymes NFκB Signaling MAP Kinase Signaling Huntington's Disease MAP Kinase Signaling Neurogenesis and Neural Stem Cell Drug Transporters T Cell Anergy & Immune Tolerance Mesenchymal Stem Cell Hypoxia Signaling mtor Signaling Neurotrophin & Receptors GPCR Signaling Finder T-cell and B-cell Activation NFκB Signaling Mesenchymal Stem Cell NFκB Signaling Notch Signaling Hepatotoxicology TGFβ BMP Signaling Osteogenesis Neurogenesis and Neural Stem Cell Nuclear Receptors and Coregulators Osteogenesis Lipoprotein Signaling & Cholesterol Metabolism Th17 for Autoimmunity and Inflammation TGFβ BMP Signaling Neuroscience Ion Channels and Transporters PI3K-AKT Signaling Stem Cell Signaling Mitochondria Th1-Th2-Th3 TNF Ligand and Receptor Neurotransmitter Receptors and Regulators Signal Transduction Finder T-cell and B-cell Activation Molecular Toxicology 384HT TNF Ligand and Receptor Tumor Metastasis Neurotrophin and Receptors TGFβ BMP Signaling Terminal Differentiation Marker Nephrotoxicity Toll-Like Receptor Signaling VEGF Signaling Nitric Oxide Signaling Transcription Factors TGFβ BMP Signaling Oxidative Stress and Antioxidant Defense Tumor Necrosis Factor (TNF) Ligand and Receptor Wound Healing Notch Signaling WNT Signaling WNT Signaling Stress and Toxicity Finder RT 2 Profiler PCR Arrays Analysis 3/211 Sample & Assay Technologies 15

16 n n n Forefront Tower II Tel: n Fax: n techservice-jp@qiagen.com /211 Sample & Assay Technologies

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