Axiom TM 2.0 Target Prep 384 Samples

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1 Quick Reference Card Axiom TM 2.0 Target Prep 384 Samples Stage 1 DNA Amplification Introduction Running the Axiom 2.0 Assay for 384 Samples Assay requires the following sets of steps: 1. Genomic DNA Prep, described in the Axiom TM 384HT gdna Sample Prep QRC (703163). 2. Target Prep of the samples, performed using Axiom 2.0 Target Prep 384 Samples, described in this QRC. 3. Array Processing, described in GeneTitan TM MC Protocol for Axiom TM 384HT Array Plate Processing QRC (P/N ). This QRC describes the automated target prep, performed using the Biomek FX P Target Prep Express. IMPORTANT: This QRC contains an abbreviated set of instructions. You must carefully read all the instructions in Chapter 3, Target Preparation with Biomek FXP Target Prep Instrument in the AxiomTM 2.0 Assay for 384 Samples User Guide (P/N ) before running the Automated Target Prep Method. The Axiom TM 2.0 Assay for 384 Samples User Guide covers the assay steps in more detail and provides information on running multiple plates per week through the automated target prep process. NOTE: The Biomek FX P should be homed before the first run of the day. If your Biomek FX P has an on deck thermal cycler for other purposes, make sure the lid is closed before homing the axes or starting a method. STAGE 1: DNA Amplification Genomic DNA Plate Preparation We recommend that you prepare your genomic DNA sample plate in a clean room. The clean room should be separate from the laboratory where the Axiom 2.0 Assay for 384 Samples Assay is performed and should be free of DNA amplified in other procedures. Time required on Biomek FX P Workstation = 30 min Plate Description Volume Deck Position Input Plate 384 Deep Well 240 µl Plate 8.7 µl P9 Output Plate 384 Deep Well 240 µl Plate µl P9 1. Performing DNA Amplification 1. Set the incubator/oven temperature at 37 C. 2. Set the centrifuge temp at room temperature. 3. Prepare reagents from Module 1 (P/N ) of the Axiom HT Reagent Kit, as shown in Table 1.1. Table 1.1: Reagents Preparation for Stage 1 Reagent Temp Out of Module* Treatment Axiom 2.0 Denat Soln 10X Thaw at Room Temp Vortex and spin Axiom 2.0 Neutral Soln Thaw at Room Temp (~1 hr) Vortex for 30 sec Axiom 2.0 Amp Soln Thaw at Room Temp (~1 hr) Vortex for 30 sec. Axiom Water (1 bottle) Thaw at Room Temp (~1 hr) Vortex Axiom 2.0 Amp Enzyme Soln Keep at 20 C Just before use, flick tube 3X, spin, and place in the cold block *Temp Out of Module: temperature reagent is held at immediately after removal from module. For Research Use Only. Not for use in diagnostic procedures.

2 4. Thaw Samples in gdna Plate: 1. Bring your gdna samples to room temperature on the bench top. 2. Vortex and spin. 3. Leave at room temperature. 5. Run Biomek method: 1. Select the DNA Amplification step, then click Run. IMPORTANT: Ensure that Test Mode is not activated. 2. Set up the deck as indicated in the deck setup prompt, scan the barcodes then click Run. NOTE: The deck setup is also shown in Figure 1.1 on the next page of this QRC. 6. When finished, remove the sample plate from the deck. 7. Blot the top of the plate with a Kimwipe. Tightly seal the plate. 8. Spin down the plate. 9. Place the sample plate in the preheated 37 C oven and incubate for 22 to 24 hr. 2. What to do Next After the incubation period, do one of the following: Proceed directly to Stage 2A Fragmentation. Check that the plate is tightly sealed and store the sample plate at 20 C Figure 1.1: Deck Layout DNA Amplification 2 Axiom TM 2.0 Target Prep 384 Samples

3 Stage 2A Fragmentation Time required on Biomek FX P Workstation = 1:20 hr Plate Description Volume Deck Position Input Plate 384 Deep Well 240 µl Plate µl P9 Output Plate 384 Deep Well 240 µl Plate µl Spelt96_1 Reagents Required Reagents from Module 2-1 (P/N ) and Module 2-2 (P/N ) of the Axiom TM HT Reagent Kit. Prepare as shown in Table 2.1 and place in the appropriate place on the deck. Table 2.1: Reagent Preparation for Stage 2A Reagent Temp Out of Module* Treatment Axiom Frag Enzyme Keep at 20 C Just before use, flick tube 3X, spin, and place in the cold block Axiom 10X Frag Buffer Thaw at Room Temp Vortex Axiom Frag Diluent Place on ice Vortex Axiom Frag Rxn Stop Room Temp Vortex *Temp Out of Module: temperature reagent is held at immediately after removal from module. NOTE: Ensure that the P-pad in deck position P4 is cleaned with 70% ethanol before and after use. 1. If frozen, Thaw the Sample Plate 1. Place the deep well plate in a small bath of room temperature Millipore water for ~ 50 min (until all wells have thawed). 2. Spin at 1000 rpm for 30 sec. 2. If Sample Plate is not frozen 1. Do not vortex. 2. Place on deck. 3. Fragment Samples 1. Run Biomek method: 1. Select Scan & Resume and scan the plate barcodes. Confirm that the Next step listed is Fragmentation. Click Resume. 2. Setup the deck as indicated the deck setup prompt, scan barcodes then click Run. NOTE: The deck layout is also shown in Figure 2.1 on the next page of this QRC. 2. When the Biomek method is finished, discard used labware, reagents, and tips from the deck. Proceed to Step 2B - Precipitation. NOTE: Fragmentation must always be followed immediately by Stage 2B Precipitation. Axiom TM 2.0 Target Prep 384 Samples 3

4 Figure 2.1: Deck Layout Fragmentation Stage 2B Precipitation Time required on Biomek FX P Workstation = 20 min Plate Description Volume Deck Position Input Plate 384 Deep Well 240 µl Plate µl P9 Output Plate Q1 96 Deep Well Square Plate µl P4 Output Plate Q3 96 Deep Well Square Plate µl P5 Output Plate Q2 96 Deep Well Square Plate µl P7 Output Plate Q4 96 Deep Well Square Plate µl P8 Reagents Required Reagents from Module 2-1 (P/N ) and Module 2-2 (P/N ) of the Axiom TM HT Reagent Kit; Isopropanol is usersupplied. Prepare as shown in Table 2.2 and place in the appropriate place on the deck. Table 2.2: Reagent Preparation for Stage 2 Reagent Temp Out of Module* Treatment Axiom Precip Soln 1 Place on ice Vortex Axiom Precip Soln 2 Thaw then place on ice Vortex and spin Isopropanol Not Applicable Room Temp *Temp Out of Module: temperature reagent is held at immediately after removal from module. 4 Axiom TM 2.0 Target Prep 384 Samples

5 IMPORTANT: During this stage, the 384 well plate of samples is split into four 96 Deep-Well Square Plates for precipitation. To avoid mislabeling samples, take care to preserve the order of the four plates and avoid interchanging these plates with those dervied from another 384-well sample plate. 1. Precipitate Samples 1. Run Biomek method: a. Select Scan & Resume and scan the plate barcodes. Confirm that the Next step listed is Precipitation. Click Resume. b. Setup the deck as indicated the deck setup prompt, scan barcodes then click Run. NOTE: The deck layout is also shown in Figure 2.2 on the next page of this QRC. 2. When the Biomek method is finished, remove the 4 precipitation plates (position P4, P5, P7, and P8) from the deck. 3. Blot the top of all 4 plates with a Kimwipe. 4. Tightly seal all 4 plates. 5. Place all 4 plates in a 20 C freezer overnight to precipitate. 2. What to do Next After overnight precipitation proceed directly to Stage 3 Centrifugation and Drying Pellets. Figure 2.2: Deck Layout Precipitation Stage 3 Centrifugation and Drying Pellets 1. Centrifuge and Dry Pellets 1. Preheat the oven to 37 C; cool centrifuge to 4 C. 2. Centrifuge the four 96-well precipitation plates at 3200 xg (or rcf) at 4 C for 40 min. Axiom TM 2.0 Target Prep 384 Samples 5

6 3. Remove the seal, then invert the plates over a waste container to allow the liquid to drain. 4. While still inverted, gently press the top of the plate on a stack of Kimwipes. 5. Leave plate inverted on Kimwipes for 5 min. 6. Turn the plates right side up and place in the preheated oven for 20 min. Plate Description Volume Deck Position Input Plate Q1 96 Deep Well Square Plate µl off deck Input Plate Q3 96 Deep Well Square Plate µl off deck Input Plate Q2 96 Deep Well Square Plate µl off deck Input Plate Q4 96 Deep Well Square Plate µl off deck Output Plate Q1 96 Deep Well Square Plate Plate Pelleted sample - off deck Output Plate Q3 96 Deep Well Square Plate Plate Pelleted sample - off deck Output Plate Q2 96 Deep Well Square Plate Plate Pelleted sample - off deck Output Plate Q4 96 Deep Well Square Plate Plate Pelleted sample - off deck 2. What to do Next After the pellets have been dried, do one of the following: Proceed directly to Stage 4A Resuspension and Hybridization Preparation (even if some droplets of liquid remain). Store plates for resuspension later in the same day: - If resuspension will be carried within 4 hours, keep the plates at room temperature. - If resuspension will be carried out in more than 4 hours, store the plates in a refrigerator (2 8 C). Store plates for resuspension on another day. Tightly seal the sample plate and store at 20 C. Stage 4A Resuspension and Hybridization Preparation Time required on Biomek FX P Workstation = 23 min Plate Description Volume Deck Position Input Plate Q1 96 Deep Well Square Plate Pelleted sample P4 Input Plate Q3 96 Deep Well Square Plate Pelleted sample P5 Input Plate Q2 96 Deep Well Square Plate Pelleted sample P7 Input Plate Q4 96 Deep Well Square Plate Pelleted sample P8 Output Plate Q1 96 Deep Well Square Plate 50 μl P4 Output Plate Q3 96 Deep Well Square Plate 50 μl P5 Output Plate Q2 96 Deep Well Square Plate 50 μl P7 Output Plate Q4 96 Deep Well Square Plate 50 μl P8 Reagents Required Prepare reagents from Module 2-1 (P/N ) and Module 2-2 (P/N ) of the Axiom TM HT Reagent Kit, as shown in Table 4.1. Table 4.1: Reagent Preparation for Stage 4A Reagent Temp Out of Module* Treatment Axiom Hyb Buffer Warm to Room Temp (~ 1 hr) Vortex Axiom Hyb Soln 1 Thaw at Room Temp Vortex and spin Axiom Resusp Buffer Warm to Room Temp (~ 1 hr) Vortex Axiom Hyb Soln 2 Warm to Room Temp (~ 1 hr) Vortex and spin *Temp Out of Module: temperature reagent is held at immediately after removal from module. 1. Prepare the Precipitation Plates Before proceeding with resuspension: Plates stored at 2-8 C after Stage 3 should be allowed to warm to room temperature for 30 min. Plates frozen at 20 C after Stage 3 should be allowed to equilibrate at room temperature for 1.5 hr. 2. Run the Biomek Method 6 Axiom TM 2.0 Target Prep 384 Samples

7 a. Select Scan & Resume and scan the barcode from any one of the four precipitation plates. Confirm that the Next step listed is Resuspension and Hyb Prep. Click Resume. b. Setup the deck as indicated in the Biomek deck setup prompt, scan barcodes then click Run. NOTE: The deck setup is also shown in Figure 4.1 on the next page. 3. Resuspend by Off Deck Shaking 1. Tightly seal the 4 plates; blue pellets should be visible at the bottom of the wells. 2. Briefly spin down the 4 plates in a room temperature centrifuge for 30 sec. 3. Place all 4 plates onto one of the following shakers for 15 min: Titer Plate Shaker 4 PL set at speed of 8. Jitterbug set at speed of Inspect the four plates from the bottom. If the pellets are not dissolved, repeat the shaking step. 5. Briefly spin down the 4 plates in a room temperature centrifuge for 30 sec. 4. What to do Next Proceed to Stage 4B Hybridization Ready Plate Reassembly and Sample QC. Figure 4.1: Deck Layout Resuspension and Hybridization Preparation Axiom TM 2.0 Target Prep 384 Samples 7

8 Stage 4B Hyb Ready Plate Reassembly and Sample QC Time required on Biomek FX P Workstation = 16 min Plate Description Volume Deck Position Input Plate Q1 96 Deep Well Square Plate 50 µl P4 Input Plate Q3 96 Deep Well Square Plate 50 µl P5 Input Plate Q2 96 Deep Well Square Plate 50 µl P7 Input Plate Q4 96 Deep Well Square Plate 50 µl P8 Output Plate 384 PCR Plate 45 µl P9 Reagents Required Reagents for this stage are user-supplied. Table 4.2. Reagent Preparation for Stage 4B Reagent Temp Out of Module* Treatment Nuclease-free water Not Applicable Not Applicable TrackIt Cyan/Orange Gel Loading Buffer (diluted 1000-fold) Not Applicable *Temp Out of Module: temperature reagent is held at immediately after removal from module. See Gel QC Instructions IMPORTANT: The four 96 Deep-Well Square Plates are reassembled into one 384 PCR Plate. To avoid mislabeling samples, ensure that the four 96-well plates are all derived from one 384 well genomic DNA sample plate and are placed on the deck in the same configuration as used in Stage 2B Precipitation. Use the barcode tracking and Scan & Resume features of the method to ensure the proper association and order of the four plates of resuspended samples. 1. Run Biomek Method 1. Select Scan & Resume and scan the plate barcodes. Confirm that the Next step listed is QC. Click Resume. 2. Setup the deck as indicated in the Biomek deck setup prompt, scan barcodes then click Run. NOTE: The deck setup is also shown in Figure 4.3 on the next page. 3. When method is finished, Tightly seal the Hyb Ready plate and store at 20 C. (This plate is referenced as Hyb Rxn in the Biomek software.) 2. Run Fragmentation QC Gels 1. Tightly seal the Gel QC plate, vortex and spin. 2. Onto a 4% agarose E-Gel TM load: 15 µl from each well of the Gel QC plate. 15 µl of 15-fold diluted TrackIt 25 bp DNA Ladder to marker wells. 15 µl water to any unused wells. Running 48 samples (one E-Gel) per 384 well plate is recommended. 3. Run for 22 min. 4. Review gel image (see Figure 4.2). 8 Axiom TM 2.0 Target Prep 384 Samples

9 Figure 4.2 Gel Image 3. Quantitate the Resuspended Samples 1. Quantitate the samples prepared in the OD plate. 2. Assess the OD reading for each sample. Median Yield = 525 µg/well 4. What to do Next If the GeneTitan MultiChannel instrument is available, and if the gel QC and quantitation results were acceptable, proceed to Stage 5 Sample Denaturation and Transfer to Hybridization Tray. Axiom TM 2.0 Target Prep 384 Samples 9

10 Figure 4.3: Deck Layout Plate Reassembly & QC Stage 5 Sample Denaturation and Transfer to Hybridization Tray Time required on Biomek FX P Workstation = 20 min Plate Description Volume Deck Position Input Plate 384 PCR Plate 45 µl P9 Output Plate 384 Hyb Tray 35 µl P8 Materials and Instruments Required Wash buffers from the Axiom 2.0 Reagent Kit - Axiom Wash A, P/N Axiom Wash B, P/N Axiom Water, P/N Hyb Ready plate from Stage 4B, Hybridization Ready Plate Reassembly and Sample QC Axiom 384-Array Plate 384 Layout GeneTitan Hyb Tray (P/N ) from the Axiom TM 384HT GeneTitan TM MC Consumable Kit (P/N ) GeneTitan MC Instrument available for hybridization Biomek FX P Target Prep Express 10 Axiom TM 2.0 Target Prep 384 Samples

11 Thermal cycler with 384-well plate adapter (See Axiom TM 2.0 Assay for 384 Samples Site Prep Guide, P/N , for recommended models) - Program with the Axiom 2.0 Denature protocol of: 95 C for 10 min; 48 C for 3 min; hold at 48 C. - Use the heated lid option when setting up or running protocols. 1. Prepare Hyb Ready Samples and Array Plate 1. Warm the array plate to room temperature for at least 25 min before setting up hybridization on the GeneTitan MC Instrument. Open the pouch and scan the barcode into the Batch Registration File at the end of the array warm up time. 2. Make sure the Hyb Ready plate is sealed well. If not, centrifuge the plate and change the seal. Evaporation can harm assay performance. If the Hyb Ready plate was stored at 20 C, warm at room temperature for 5 minutes before checking the seal. 3. Vortex the Hyb Ready plate briefly, then spin at 1000 rpm for 30 seconds. 4. Leave the Hyb Ready plate at room temperature. 2. Perform Denaturation Using Off Deck Thermal Cycler 1. Place Hyb Ready plate in thermal cycler block, secure lid and start the Axiom 2.0 Denature program. 2. While the program is running: Upload the Batch Registration File. Set up the GeneTitan MC Instrument. For more information, see: - GeneTitan TM MC Protocol for Axiom TM 384HT Array Plate Processing QRC (P/N ). - Chapter 4, Array Processing with the GeneTitan TM Multi-Channel Instrument of the Axiom 2.0 Assay for 384 Samples User Guide (P/N ). 3. Run the Biomek Method 1. Select Scan & Resume and scan the plate barcodes. Confirm that the Next step listed is Transfer Samples to Hyb Tray. Click Resume. 2. Setup the deck as indicated in the Biomek deck setup prompt, scan barcodes then click Run. NOTE: The deck setup is also shown in Figure 5.1 on the next page. 3. Load Hyb Tray and Array Plate into the GeneTitan MC Instrument. 4. What to do Next Near the end of the 23.5 to 24 hour hybridization period in the GeneTitan MC Instrument, proceed to Stage 6 GeneTitan Reagent Prep on the Biomek FX P. Figure 5.1: Deck Layout Sample Denaturation & Transfer to Hybridization Tray Axiom TM 2.0 Target Prep 384 Samples 11

12 Stage 6 GeneTitan TM Reagent Prep on the Biomek FX P Important Guidelines for this Stage The reagent trays prepared in this stage are for the continued processing of an Axiom array plate that is: already on the GeneTitan MC Instrument. has completed the hybridization stage. is ready for transfer to the fluidics area. Begin deck setup for this stage 70 to 80 min prior to when the array plate currently in the GeneTitan TM MC Instrument will finish hybridization. This step of the method on the Biomek FX P takes approximately 55 min to run. The reagent trays for the fluidics stage on the GeneTitan TM MC Instrument CANNOT be prepared in advance. Do not prepare these plates if there is no array plate ready for the fluidics stage. Once prepared, these plates must be loaded onto the instrument as soon as possible and cannot be stored. Prepare Reagent Trays for the GeneTitan Instrument 1. Prepare the reagents from Module 4 of the Axiom TM HT Reagent Kit, as shown in Table 6.1 below (requires 2 each of the reagents listed). Table 6.1: Reagent Preparation Module 4-1, 20 C (P/N ) Reagent Temp Out of Module* Treatment Axiom Ligate Buffer Thaw at Room Temp 1. Place on bench top at room temp for 30 min 2. Vortex twice 3. Examine for precipitate If any: Warm bottle with your hands and vortex again for thirty seconds Axiom Ligate Enzyme Keep at 20 C until ready to use Just before use: 1. Flick 2 to 3 times to mix 2. Spin 3. Place in the cold block Axiom Ligate Soln 1 Thaw at Room Temp Vortex and Spin Axiom Probe Mix 1 Thaw at Room Temp Vortex and Spin Axiom Stain Buffer Thaw at Room Temp Vortex and Spin Axiom Stabilize Soln Thaw at Room Temp Vortex and Spin Module 4-2, 2-8 C (P/N ) Axiom Ligate Soln 2 Thaw at Room Temp (do not place on ice!) Vortex and Spin Axiom Probe Mix 2# Place on Ice Flick 2 to 3 times to mix, then spin Axiom Wash A Leave on bench 1. Vortex twice 2. Place on Bench for 30 min 3. Look for precipitate 4. Vortex again if necessary Axiom Stain 1-A# Place on ice Flick 2 to 3 times to mix, then spin Axiom Stain 1-B# Place on ice Flick 2 to 3 times to mix, then spin Axiom Stain 2-A# Place on ice Flick 2 to 3 times to mix, then spin Axiom Stain 2-B# Place on ice Flick 2 to 3 times to mix, then spin Axiom Stabilize Diluent Place on ice 1. Vortex and Spin 2. Look for precipitate If any: Warm tube to room temperature and vortex again Axiom Water Place on ice N/A Axiom Hold Buffer# (1 bottle) Room Temp Vortex Notes: * Temp Out of Module: temperature the reagent is held at immediately after removal from module. # These solutions are light sensitive. Keep tubes out of direct light for a prolonged period of time. N/A: not applicable in this case. 2. Run Biomek method: a. Select Scan & Resume and scan the plate barcodes. Confirm that the Next step listed is GT Reagent Prep. Click Resume. 12 Axiom TM 2.0 Target Prep 384 Samples

13 b. Setup the deck as indicated in the deck setup prompt, scan barcodes then click Run. The deck setup is also shown in Figure 6.1 of this QRC. The stain trays, scan tray, and covers come from the Axiom TM 384HT GeneTitan TM MC Consumable Kit (P/N ) IMPORTANT: Label the stain trays to aid in correct loading of the GeneTitan MC Instrument. 3. Prepare the GeneTitan TM Multi-Channel Instrument. See GeneTitan TM MC Protocol for Axiom TM 2.0 Array Plate Processing QRC (P/N ). 4. Cover the reagent plates and Scan Tray with lids. 5. Examine each tray to ensure that all wells contain reagents (manually add if not present) and puncture any bubbles with a clean pipette tip. 6. Immediately load the reagent plates and Scan Tray into the the GeneTitan Instrument. See GeneTitan TM MC Protocol for Axiom TM 2.0 Array Plate Processing QRC (P/N ). Figure 6.1: Deck Layout GeneTitan Reagent Prep on Biomek FX P Axiom TM 2.0 Target Prep 384 Samples 13

14 Documentation and support Customer and technical support Visit thermofisher.com/support for the latest in services and support, including: Worldwide contact telephone numbers Product support, including: - Product FAQs - Software, patches, and updates Order and web support Product documentation, including: - User guides, manuals, and protocols - Certificates of Analysis - Safety Data Sheets (SDSs; also known as MSDSs) Limited product warranty Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale found on Life Technologies' website at If you have any questions, please contact Life Technologies at thermofisher.com/support. Note: For SDSs for reagents and chemicals from other manufacturers, contact the manufacturer. 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. Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept the terms and conditions of all applicable Limited Use Label Licenses. Corporate entity: Life Technologies Carlsbad, CA USA Toll Free in USA Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. All other trademarks are properties of their respective owners. P/N For support visit thermofisher.com/support or techsupport@lifetech.com thermofisher.com 23 January 2017

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