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Pharmacoscan Assay 24-Array Format Manual Workflow  Equipment Manufacturer Cat PharmacoScan™ Assay 24-Array Format Manual Workflow SITE PREPARATION GUIDE Catalog Numbers 902908TS and 902994 Publication Number 703287 Revision 4 For Research Use Only. Not for use in diagnostic procedures. Thermo Fisher Scientific Baltics UAB Products: PharmacoScan™ Reagent Kit V.A. Graiciuno 8, LT-02241 Vilnius, Lithuania Affymetrix Pte Ltd Products: PharmacoScan™ Array Plates 7 Gul Circle #2M-01 Keppel Logistics Building Singapore 629563 The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT. Revision history: Pub. No. 703287 Revision Date Description 4 17 May 2018 Updated to include an option for a three-hour DNA precipitation step to enable faster assay turnaround time. 3 30 January 2018 Updated to the current document template, with associated updates to the warranty, trademarks, and logos. Two additional sample types have been validated and added to the document: saliva and buccal cell. 2 05 October 2016 Baseline for revision history. Important Licensing Information This product may be covered by one or more Limited Use Label Licenses. By use of this product, you accept the terms and conditions of all applicable Limited Use Label Licenses. Corporate entity Life Technologies | Carlsbad, CA 92008 USA | Toll Free in USA 1 800 955 6288 TRADEMARKS All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. ©2018 Thermo Fisher Scientific Inc. All rights reserved. Contents CHAPTER 1 Equipment and supplies required . 4 Equipment, software, reagents, and arrays required . 4 Equipment required for manual target preparation . 6 Preamplification area/amplification staging area . 6 Oven requirements . 7 Spectrophotometer . 7 Thermal cycler recommendations and protocols . 8 Thermal cycler consumables . 9 Plate centrifuge . 9 Sample plates . 10 Pipettes and tips . 11 Other labware required . 12 Other reagents and gels required . 12 Other lab equipment required . 13 APPENDIX A Supplier Contact List. 14 Related documentation . 15 Customer and technical support . 16 Limited product warranty . 17 PharmacoScan™ Assay 24-Array Format Manual Workflow Site Preparation Guide 3 1 Equipment and supplies required This site preparation guide includes the supplier and part number information for the equipment, software, reagents, arrays, labware and other consumables that have been validated for use with the PharmacoScan™ Assay 24-Array Format Manual Workflow. Information on suppliers of the equipment and supplies is listed in Appendix A, ʺSupplier Contact Listʺ on page 14. Equipment, software, reagents, and arrays required Table 1 Equipment, software, reagents, and arrays required Item Cat. No. Equipment GeneTitan™ Multi-Channel Instrument1 Contact Thermo Fisher Scientific Software GeneChip™ Command Console™ (GCC) version 4.3 or later Axiom™ Analysis Suite version 3.0 or later Reagents PharmacoScan™ Reagent Kit 4x24 Reactions (one required) 902908TS Each PharmacoScan Reagent Kit 4x24 Reactions contains the following modules for processing four 24-array format plates: • PharmacoScan Module A (quantity one, contains four vials) • 902896 • PharmacoScan Module B (quantity one, contains four vials) • 902897 • Module 1 (quantity one) • 901711 • Module 2-1 (quantity one) • 901528 • Module 2-2 (quantity one) • 901529 • Module 3 (quantity four) – Wash Buffer A – 901446 – Wash Buffer B – 901447 – Water – 901578 • Module 4-1 (quantity one) • 901278 • Module 4-2 (quantity one) • 901276 • Module 5-1 (quantity one) • 902796 • Module 5-2 (quantity one) • 902797 4 PharmacoScan™ Assay 24-Array Format Manual Workflow Site Preparation Guide Chapter 1 Equipment and supplies required Equipment, software, reagents, and arrays required 1 Table 1 Equipment, software, reagents, and arrays required (Continued) Item Cat. No. Arrays PharmacoScan™ 24F Array Plates (four) 902994 PharmacoScan™ Array GeneTitan Consumables Each Axiom™ GeneTitan™ Consumables Kit contains the following labware for each array 901606 plate: • One hybridization tray • One scan tray with top cover and protective base • Five stain trays with top covers These trays are required for processing PharmacoScan array plates on the GeneTitan™ Multi-Channel Instrument. * For a complete list of all equipment and supplies required for GeneTitan Instrument installation and operation, please consult the GeneTitan™ Multi-Channel Instrument Site Preparation Guide (Pub. No. 08-0305). PharmacoScan™ Kits PharmacoScan™ Training 24F Kit for Manual Workflow 903011TS Each Kit Includes: • PharmacoScan™ Reagent Kit 4x24 Reactions • Four PharmacoScan™ 24F Array Plates • Four Axiom™ GeneTitan™ Consumables Kits • Two PharmacoScan™ DNA Training Plates, for 24-format Assay PharmacoScan™ Assay 24F Kit for Manual Workflow 903010TS Each Kit Includes: • PharmacoScan™ Reagent Kit 4x24 Reactions • Four PharmacoScan™ 24F Array Plates • Four Axiom™ GeneTitan™ Consumables Kits PharmacoScan™ Assay 24-Array Format Manual Workflow Site Preparation Guide 5 Chapter 1 Equipment and supplies required 1 Equipment required for manual target preparation Equipment required for manual target preparation Table 2 Additional instruments required for the PharmacoScan™ Assay 24-Array Format Manual Workflow Equipment Manufacturer/ Cat. No. distributor Two ovens (see "Oven requirements" on page 7) Fume hood (Strongly recommended: see the PharmacoScan™ Assay 24-Array Format Manual Workflow User Guide for more information) Thermal cycler: • Applied Biosystems 9700 Thermo Fisher Scientific • Applied Biosystems Veriti™ Thermo Fisher Scientific • Applied Biosystems ProFlex™ Thermo Fisher Scientific • Eppendorf Mastercycler™ pro S Eppendorf (see "Thermal cycler recommendations and protocols" on page 8) One of the following shakers: • Compact Digital Microplate Shaker Thermo Scientific 88880023 •Jitterbug™ Boekel Scientific Model 130 000 Preamplification Precautions are required when manipulating genomic DNA or setting up area/amplification amplification reactions to avoid contamination with foreign DNA amplified in other staging area reactions and procedures. It is recommended that genomic DNA manipulations and amplification reaction set up are performed in a dedicated rooms or areas separate from the main laboratory. These areas should have dedicated sets of pipettes and plasticware. If no dedicated area is available, use of a dedicated bench or a dedicated biosafety hood and dedicated pipettes is suggested. If no dedicated bench or biosafety hood is available, a set of dedicated pipettes is recommended. Ideally, the pre-amplification and amplification staging areas would be separate; however these areas may be combined due to space and equipment limitations. 6 PharmacoScan™ Assay 24-Array Format Manual Workflow Site Preparation Guide Chapter 1 Equipment and supplies required Equipment required for manual target preparation 1 Oven requirements Two ovens are required for PharmacoScan manual target preparation using the standard overnight DNA precipitation workflow. If you are running the three-hour precipitation workflow, a third oven is highly recommended. Table 3 Ovens required for the PharmacoScan Assay 24-Array Format Manual Workflow Equipment Manufacturer Cat. No. Two ovens, any combination of the following types: • ED 56 Drying and Heating Chamber1 BINDER ED056UL-120V Voltage: 120 V 1~60 Hz P/N 9010-0334 ED056-230V Voltage: 230 V 1~50/60 Hz P/N 9010-0333 • GeneChip™ Hybridization Oven 6452 Thermo Fisher Scientific 00-0331 1 Replaces BINDER Model ED 53. 2 The GeneChip™ Hybridization Oven 640 is currently not supported with the PharmacoScan Assay 24-Array Format Manual Workflow. Spectrophotometer We recommend using one of the spectrophotometers listed in Table 4. Table 4 Spectrophotometers Item Supplier Cat. No. One of the following spectrophotometers: • DTX 880 Multimode Detector, with: Beckman Coulter 987921 – detector – Genomic Filter Slide Beckman Coulter A30184 – filter slide or • SpectraMax High Throughput Microplate Molecular Plus384 Spectrophotometer Devices PharmacoScan™ Assay 24-Array Format Manual Workflow Site Preparation Guide 7 Chapter 1 Equipment and supplies required 1 Equipment required for manual target preparation Thermal cycler The following thermal cyclers have been validated for the PharmacoScan Assay 24- recommendations Array Format Manual Workflow: and protocols • Applied Biosystems 9700 (with gold-plated or silver block) • Applied Biosystems Veriti • Applied Biosystems ProFlex • Eppendorf Mastercycler pro S IMPORTANT! Always use the heated lid option when programming protocols. The PharmacoScan mPCR protocol was validated using the “9600 mode” on the Applied Biosystems 9700, Applied Biosystems Veriti, and Applied Biosystems ProFlex thermal cyclers. The “Safe” mode was used for the Eppendorf Mastercycler pro S. Refer to the manufacturer’s user guide for programming information. Figure 1 PharmacoScan mPCR thermal cycler protocol (Stage 1A) Figure 2 PharmacoScan Denature thermal cycler protocol (Stage 4) WARNING! Evaporation during denaturation can negatively impact assay performance. Use the recommended thermal cycler consumables and sealing film to eliminate condensation and evaporation. PharmacoScan Assay 24-Array Format Manual Workflow has been validated with the Applied Biosystems 9700 (with
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