axiom 2.0 assay 384ht-array format · • 15 x 384 deep-well 240 μl plate (part no. 203017) • 15...

Axiom™ 2.0 Assay 384HT-Array FormatSITE PREPARATION GUIDE

Automated Protocol for Beckman Biomek FXP

Publication Number 703269

Revision 5

For Research Use Only. Not for use in diagnostic procedures.

The information in this guide is subject to change without notice.

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Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Site Prepa

Contents

CHAPTER 1 Biomek® FXP Target Prep Express Configuration . . . . . . . 4

Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Instrument specifications and settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Related Beckman Coulter documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Axiom™ 2.0 Target Prep Method for 384 Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Importing the method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

CHAPTER 2 Equipment and supplies required . . . . . . . . . . . . . . . . . . 10

Applied Biosystems equipment, software, reagents, and arrays required . . . . . . . . . . . . . . 10

Labware required for the Biomek FXP Target Prep Express. . . . . . . . . . . . . . . . . . . . . . . . 13

Axiom™ 2.0 Target Prep 384HT Samples Templates Kit . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Other equipment, consumables, and reagents required . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Pre-amplification area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Oven requirements for target prep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Spectrophotometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Thermal cyclers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Shakers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Plate centrifuge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Other common lab equipment required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Other reagents and gels required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Pipettes and tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Other Consumables Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

APPENDIX A Supplier contact list. . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

ration Guide 3

1 Biomek® FXP Target Prep ExpressConfiguration

Equipment

The Beckman Coulter Biomek® FXP Target Prep Express (Cat. No. A83103) is required to run the Axiom™ 2.0 Assay for 384HT Samples with the automated target preparation. This workstation includes the accessories, software and deck configuration listed in Table 1. For information on upgrading a Biomek liquid handler already at your site, contact Beckman Coulter. In addition to this workstation, the components listed in Chapter 2 are also required. This chapter details the configuration required when using Windows® 7 operating system.

Table 1 Biomek FXP Target Prep Express for Running the Axiom™ 2.0 Assay for 384HT Samples Workflow

Item Quantity BeckmanCat. No.

Biomek FXP Target Prep ExpressThe part number for this workstation includes the components listed below.

1 A83103

• Biomek FXP Dual Multichannel Span-8 1 A31844

• Biomek Windows 7 New Installation kit with Biomek Software 4.1 1 B40917

• Packaged Tip Loader 1 719356

• Span-8 Disposal ALP 1 719590

• Low Volume Disposable Mandrel Kit 8-Pack 1 A39380

• BFX 96-channel Disp, Tip Head, 200U 1 719368

• Pkg Static ALP Platform 4 719357

• 4 × 3 ALP Kit 1 719948

• Static Peltier ALP 1 A93938

• Shaking Peltier ALP 1 A93942

• Adapter, Deep Well Plate (required for Axiom™ assays) 1 A83050

• Adapter, Thin PCR (required for HT 3' IVT PLUS and HT WT PLUS assays) 1 A19709

• Frame for Modular Reservoir 4 372795

• 24-Position Tube Rack 1 373661

• Inserts, Tube, 11 mm (case of 25) 1 373696

• 24 Position Cold Tube Block(referred to as Reagent Cold Block in this document)

1 A83054

4 Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Site Preparation Guide

Chapter 1 Biomek® FXP Target Prep Express ConfigurationInstrument specifications and settings 1

Instrument specifications and settings

In order for the Axiom 2.0 assay for 384HT Samples to be successfully performed on the Biomek FXP Target Prep Express Instrument the system must meet the following specifications and be properly configured.

• Biomek FXP Target Prep Express system

– Hybrid dual armed Biomek FXP

– 96MC head left pod and Span-8 head right pod

– 1 mL syringes and low volume tubing on the Span8 system

– 384 Deep-Well Adapter (Cat. No. 101019) mounted on the Shaking Peltier Device with notches facing the front

– ALPs secured to deck as shown in Figure 1

• System fluid is degassed water

• Clean compressed air is at 40–80 psi

• Computer workstation specifications

– Windows® 7 operating system

– Internet Explorer® v8.0

– Microsoft® Excel® 2010 software; 32-bit version ONLY software

– Biomek software v4.1.41 (version 4.1 build 41)

• Biomek software

– Make sure that the Affymetrix Deck is the default deck

– Make sure deck location SPelt96_1 has the device ShakingPeltier1 associated with it

– Make sure deck location Pelt_1 has the device StaticPeltier1 associated with it

– Make sure deck location TR1 is ALP type Span8TrashRight and not Span8TipTrashRight

• Check for a properly framed deck for both the Biomek FXP 96MC and Span8 pods

– Framing tolerance is 0.03 cm. Reframe if this is exceeded when checked

– If deck was reframed, save a current copy of the instrument file for backup

– Exit and restart Biomek software after installing Affymetrix Deck and after any changes in deck framing in order to save the new values in the default instrument (.bif) file

• Additional Pod Settings

– Navigate to: Instrument Hardware Setup Pod2 Additional Pod Settings

– Pod 2 (Span-8) settings: Set System Trailing Airgap to 20 µL (Figure 2)

– Pod 1 (MC96) settings (Figure 3):

Check Always Rove at Z-Max box

Set Additional Roving Height to 0.45 cm or lower (default is 0.75 cm)

Set Gripper Offset in D Axis to 0.7 cm

Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Site Preparation Guide 5

Chapter 1 Biomek® FXP Target Prep Express ConfigurationInstrument specifications and settings1

Figure 1 Biomek FXP TPE System (top) and Deck Configuration (bottom)


Chapter 1 Biomek® FXP Target Prep Express ConfigurationInstrument specifications and settings 1

Figure 2 Hardware Setup Changes for Span-8 Pod2

Figure 3 Hardware Setup Changes for Multichannel 96 Pod1


Chapter 1 Biomek® FXP Target Prep Express ConfigurationRelated Beckman Coulter documentation1

Related Beckman Coulter documentation

• Biomek® Liquid Handler User’s Manual, Beckman Coulter Pub. No. 987834

• Biomek® FX Laboratory Automation Workstation Preinstallation Manual, Beckman Coulter Pub. No. 719450, rev AH

• Biomek® Software User’s Manual Version 4.1, Beckman Coulter Pub. No. B30026AA

• Install Guide Biometra TRobot on Biomek FX Revision 2, 9/8/2014

Axiom™ 2.0 Target Prep Method for 384 Samples

The purpose of this section is to identify critical steps for importing the Axiom™ 2.0 Target Prep 384 Samples method into the Biomek® software for use on the Biomek® FXP Target Prep Express.

Importing the method

1. Run Setup.exe.

2. Click Setup.exe in method package to copy files from the package to the following locations and import the Biomek method.

Table 2 Directory Location

Source Destination

\Root\*.* C:\Users\Public\Documents\Affymetrix\Axiom 2.0 384

\Images\ C:\Users\Public\Documents\Axiom 2.0 384\Images

\Misc\ C:\Users\Public\Documents\Axiom 2.0 384


Chapter 1 Biomek® FXP Target Prep Express ConfigurationAxiom™ 2.0 Target Prep Method for 384 Samples 1

3. Set Method Preferences:

a. Locate and click the method branch named Axiom 2.0 Target Prep 384 Samples (Figure 4).

b. Barcode Tracking [Enabled] to input barcode during runtime deck setup.

• Log Name [Default/Other]: Name of barcode log text file

• Log Path [Default/Other]: Location of barcode log file

c. Set the Validate Reagent Module Barcodes run option to check for the correct reagent module part number.

d. Set the Verify GeneTitan Labware Setup run option to check if the GT trays were placed in the correct position on the deck.

e. Set the Prepare gel and OD plates for QC run option.

f. Set the Test Mode run option which disables the timers.

Figure 4


2 Equipment and supplies required

This chapter includes the supplier and ordering information for the equipment, software, reagents, arrays, labware and other consumables that have been validated for use with the Applied Biosystems™ Axiom™ 2.0 Assay for 384HT Samples.

Information on suppliers of the equipment and supples is listed in Appendix A, ʺSupplier contact listʺ on page 27.

Applied Biosystems equipment, software, reagents, and arrays required

Table 3 Applied Biosystems equipment, software, reagents and arrays required

Item Cat. No.

Equipment

GeneTitan™ Multi-Channel Instrument* Contact Thermo Fisher Scientific, Inc.

Software

GeneChip™ Command Console™ (AGCC) version 4.3 or later

Axiom Analysis Suite version 1.1 or later

Reagents

Axiom™ 2.0 384HT Reagent Kit 902245 (Sufficient for one 384HT array plate)

Arrays

Axiom™ 384HT Genotyping Solution Array Plates:

Please visit www.thermofisher.com for a complete list of array plates available for use with the Axiom™ 2.0 Assay for 384 Samples.

* For a complete list of all equipment and supplies required for GeneTitan Instrument installation and operation, please consult theGeneTitan™ Multi-Channel Instrument Site Preparation Guide (Pub. No. 08-0305).


http://www.affymetrix.com

Chapter 2 Equipment and supplies requiredApplied Biosystems equipment, software, reagents, and arrays required 2

Consumables

Each Axiom™ 384HT High Volume Consumable Kit is sufficient to process 5 Axiom 384-format plates. • 10 x 384 Layout GeneTitan™ Stain Tray (Stain 1)• 5 x 384 Layout Axiom™ Stain 2 Tray• 5 x 384 Layout Axiom™ Stab. Tray• 5 x 384 Layout Axiom™ Ligation Tray• 5 x 384 Layout GeneTitan™ Hyb Tray• 5 x 384 Layout GeneTitan™ Scan Tray• 25 x 384 Layout GeneTitan™ Scan and Stain Tray Cover These trays are required for processing Axiom 384 array plates on the GeneTitan™ Multichannel Instrument. Please use the new Axiom 384HT High Volume Consumable Kit when running the Applied Biosystems™ Axiom™ 2.0 Assay for 384HT Samples.

902629

Axiom™ 384HT Consumable Kit for Biomek FXp (sufficient for 5 x 384 rxn runs)1 2

Each Kit Includes:• 10 x 96 PCR Plate (Part No. 203015)• 20 x 96 Deep-Well Square Plate (Part No. 203016)• 15 x 384 Deep-Well 240 μL Plate (Part No. 203017)• 15 x 384 Standard 120 μL Plate (Part No. 203018)• 5 x 384 PCR Plate (Part No. 902288)• 35 x Shallow 96 Full Reservoir (Part No. 203020)• 5 x Deep 96 Full Reservoir (Part No. 203021)

902288

Axiom™ 384HT Consumable Kit for QC (sufficient for 10 x 384 rxn runs)2, Each Kit Includes:• 10 x 384 UV Plate (Part No. 203022)

902289

Axiom™ 384HT Starter kit for Biomek FXP Each Kit Includes:• 1 x Thermoshake 384 Adapter (Part No. 101019)• 1 x Plastic Plate Lid (Part No. 101018)• Plate collar• 1 set Reservoir Stickers (Part No. 90-0972)• 1 x Cold Block Template #1 (Part No. 15-0448)• 1 x Cold Block Template #2 (Part No. 15-0451)• 1 x 2D Handheld Barcode Reader (Part No. 00-0179) • 1 x External Barcode Reader Holder (Part No. 00-0093)

902290

Training Modules Available

Axiom™ 384HT Training Kit, Each Kit Includes:• Axiom™ 2.0 384HT Reagent Kit.• Axiom™ Human AIMs Array Plate• Axiom™ 384HT Consumable Kit for Biomek FXP • Axiom™ 384HT Consumable Kit for QC • Axiom™ 384HT GeneTitan™ MC Consumable Kit• HapMap Samples3

902291

1 For quantity required per run, please refer to Table 4.2 The components of this kit may be purchased directly from the vendor, as listed in Table 4.

Table 3 Applied Biosystems equipment, software, reagents and arrays required (Continued)

Item Cat. No.


Chapter 2 Equipment and supplies requiredApplied Biosystems equipment, software, reagents, and arrays required2

3 Note: Per Thermo Fisher Scientific agreement with Coriell, all residual HapMap DNA samples must be destroyed immediately followingcompletion of training.



Labware required for the Biomek FXP Target Prep Express

The labware required to run the Axiom™ 2.0 Assay for 384HT Samples Workflow on the Biomek FXP Target Prep Express is listed in Table 4. Photographs of the labware are provided in Table 5 on page 14.

Table 4 Labware for the Biomek FXP Target Prep Express

Item Quantity required Supplier Cat. No.

Pipette tips, barrier, 96 tips/rack1

AP96 P50 Tips (pink) 1152 tips

Beckman Coulter

A21586

AP96 P250 Tips (aqua) 1440 tips 717253

Span-8 P250 Tips (green) 50 tips 379503

Span-8 P1000 Tips (yellow) 154 tips 987925

Plates

96 PCR Plate2 2 BIO-RAD HSP9631

384 Deep-Well 240 μL Plate2 3 3 E&K Scientific EK-2010-SBC

384 Standard 120 μL Plate2 3 Axygen/Corning P-384-120SQ-C

384 PCR Plate2,3 1 Thermo Fisher Scientific

902288

96 Deep-Well Square Plate2, 3 4 Thermo Scientific

AB-0932

384 UV Plate4 1 E & K Scientific EK-30801

Reservoirs for Reagents

Shallow 96 Full Reservoir2 7 E & K Scientific EK-2036

Deep 96 Full Reservoir2 1 E & K Scientific EK-2035

Half Reservoir (75 mL module) 2Beckman Coulter

372786

Quarter Reservoir (40 mL module) 13 372790

Quarter Reservoir Divided by Width (19 mL module) 1 372792

Other

Microseal 'P' Replacement Pads BIO-RAD MSP-1003

Plastic Plate Lid Thermo Fisher Scientific

101018

384 Deep-Well Adapter Thermo Fisher Scientific

101019

1 For pipette tips, the “Quantity required” column lists the total number of tips required and not the number of racks.2 Available in the Axiom™ 384HT Consumable kit for Biomek FXP (Cat. No. 902288). See Table 3 on page 10 for details.3 This plate is also part of the Axiom™ 384HT Consumable kit for Biomek® FXP. If purchased directly from the supplier, a unique barcode

must be added.4 Available in the Axiom™ 384HT Consumable Kit for QC (Cat. No. 902289). See Table 3 on page 10 for details.



Photographs of the labware requiredThe photographs in Table 5 are provided to help visualize the labware required on the Biomek FXP Target Prep Express to run the automated target preparation portion of the Axiom™ 2.0 Assay Automated Workflow.

Table 5 Labware Used on the Biomek Workstation deck

Labware Supplier and Cat. No. Labware image

Biomek AP96 – P250 Pipette Tips (aqua box; pre-sterile, barrier)

Beckman CoulterCat. No. 717253

Biomek Span P250 Pipette Tips (green box; pre-sterile, barrier)


Biomek Span P1000 Pipette Tips (yellow box; pre-sterile, barrier, conductive)


Biomek Span P50 Pipette Tips (pink box; pre-sterile, barrier)

Beckman CoulterCat. No. A21586



Frame for reservoirs Beckman CoulterCat. No. 372795

Half reservoirHalf module, 75 mL capacity


Quarter reservoirs• Quarter module, 40 mL capacity• Quarter module divided by width,

19 mL capacity each receptacle

Beckman Coulter• Cat. No. 372790 (40 mL)• Cat. No. 372792 (19 mL)

Table 5 Labware Used on the Biomek Workstation deck (Continued)


Frame

Divided by width19 mL capacity

Undivided40 mL capacity



Reagent block, chilled to 4°C Beckman CoulterCat. No. A83054

24-position tube rackwith two 11 mm tube inserts in positions A1 and B1.

Beckman CoulterCat. No. 373661 (rack)Cat. No. 373696 (insert)

Plate collar Plate collar used with ABgene 384-well PCR plate. Contact your Genotyping Technical Sales Specialist for additional plate collars.

96 PCR plateHard-Shell® Thin-Wall96-Well Skirted PCR Plates(available in multiple colors)

Bio-RadCat. No. HSP9631

Also available in the Axiom™ 384HT Consumable kit for Biomek FXP (Cat. No. 902288)



Metal posts on block circled in red.A1



384 deep-well 240 μL plate1

Axygen® 384 Well Clear V-Bottom 240 μL Polypropylene Deep Well Not Treated Plate, Sterile

Axygen/CorningCat. No. P-384-240SQ-C-S


384 standard 120 μL plateAxygen® 384 Well Clear V-Bottom 120 μL Polypropylene Deep Well Not Treated Plate

Axygen/CorningCat. No. P-384-120SQ-C


384 PCR Plate2 ABgene 384 Well PCR Microplate, Clear, Nonsterile

Thermo Fisher ScientificCat. No. AB0937


96 deep-well square plate1 ABgene® Mark II 96-Well Storage Plate, Square Well, 2.2 mL

Thermo ScientificCat. No. AB-0932






384 UV plate384 Well, UV-Star Plates 120 μL, Non-Sterile

E & K ScientificCat. No. EK-30801

Also available in the Axiom™ 384HT Consumable kit for QC (Cat. No. 902289)

Shallow 96 full reservoir Individual Well Format Reservoirs - 96 Well, Low Profile



Deep 96 full reservoir Individual Well Format Reservoirs - 96 Well, Sterile



Plastic plate lid Thermo Fisher Scientific Cat. No. 101018

Also available in Axiom™ 384HT Starter kit for Biomek FXP (Cat. No. 902290)



Plastic plate lid (top side)

Plastic plate lid (underside)

P-pad



P PadMicroseal® ‘P’ PadPCR plate-sealing pad for automation, resusable

Bio-RadCat. No. MSP-1003

384 deep-well adapterPlate adapter for Inheco Thermoshake, fits Axygen P-384-240SQ-C-S 384 deep-well plate

Thermo Fisher ScientificCat. No. 101019

Also available in Axiom™ 384HT Starter kit for Biomek FXP (Cat. No. 902290)

1 The plates come unbarcoded from the vendor. Barcode labels should be applied before use. Barcoded versions of the plates areavailable in the Axiom 384HT Consumable Kit for Biomek FXP.

2 At the current time this plate is unbarcoded. If desired, barcode label must be manually applied.





Axiom™ 2.0 Target Prep 384HT Samples Templates Kit

The Tube Block and Reservoir Frames templates are provided in the Axiom™ 384HT Starter Kit for Biomek FXP (Cat. No. 902290) and are ordered by your Thermo Fisher Scientific FAS prior to beginning training. These templates are used with the automated target prep protocol.

Tube block templateThe Axiom 2.0 Target Prep 384 Samples Reagent Kit tube block templates were designed to fit precisely onto the top of the Beckman Coulter Tube Block (Cat. No. A83054). They are held in place by the metal posts on the block (Figure 5). Using these templates helps to ensure the proper placement of reagent tubes onto the block for each method.

Reservoir labelsThe reservoir labels are stick-on labels for the modular reagent reservoir frames (used at different stages in the automated workflow) and are provided in the Axiom™ 2.0 Target Prep 384HT Samples Templates Kit. These stick-on labels are color-coded to match the colors found on the caps of the reagent tubes in the Axiom 2.0 384HT Reagent Kit. Using these labels helps ensure the proper placement of reservoirs and reagents for each step.

Figure 5 Axiom Reagent Templates for Tube Block

Tube block templates

Tube block



There are three reservoir holders used in the Axiom 2.0 Target Prep 384 Samples method. Two of these will have templates on two sides and the remaining reservoir holder will have a template on one side for a total of 7 templates.

Remove the protective surface from the back of the label and place on the reservoir frames as directed in the Figure 6 through Figure 8.

Reservoir frame 1

Reservoir frame 2

Figure 6 Reservoir frame 1



Chapter 2 Equipment and supplies requiredOther equipment, consumables, and reagents required2

Reservoir frame 3

Other equipment, consumables, and reagents required

Pre-amplification area

Precautions are required when manipulating genomic DNA to avoid contamination with foreign DNA amplified in other reactions and procedures. It is recommended that genomic DNA manipulations are performed in a dedicated pre-amplification room or area separate from the main laboratory.

This pre-amplification area should have a dedicated set 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.

Oven requirements for target prep

We recommend using the ED 56 BINDER oven listed in Table 6. If another oven is used, it must be able to maintain a constant temperature of 37°C for at least 24 hr, and have a temperature accuracy of 1°C.


Table 6 Ovens Required for the Axiom 2.0 Assay for 384HT Samples

Item Supplier Cat. No.

Oven:

Required if processing more than 3 array plates per week.

• ED 56 Drying and Heating Chamber1 BINDER ED056UL-120VVoltage: 120 V 1~60 Hz

P/N 9010-0334

ED056-230VVoltage: 230 V 1~50/60

HzP/N 9010-0333

Optional — for low throughput of 3 or fewer array plates per week:• GeneChip™ Hybridization Oven 6452 Thermo Fisher

Scientific00-0331

1 Replaces BINDER Model ED 56.2 The GeneChip™ Hybridization Oven 640 is currently not supported with the Axiom 2.0 Assay; however, if you want to utilize it in the

workflow please contact your Field Service Engineer (FSE) or Thermo Fisher Scientific Technical Support regarding the compatibility ofthis oven with the Axiom 2.0 Assay.


Chapter 2 Equipment and supplies requiredOther equipment, consumables, and reagents required 2

Spectrophotometer We recommend using one of the spectrophotometers listed in Table 7.

Thermal cyclers We have verified the performance of this assay using the following off-deck thermal cyclers in their 384-well block configurations:

• Dual 384-Well GeneAmp® PCR System 9700, Cat. No. N8050002

• For existing GeneAmp® PCR System 9700 the following 384 block module can be used with the assay

– Dual 384-Well Sample Block Module, Cat. No. N8050400 BI 9700 (with a gold, silver or aluminum block)

The performance of this assay has not been verified with other thermal cyclers. Use of other thermal cyclers may result in assay failure and may violate the Axiom Array and Reagent replacement policy.

Shakers We recommend using one of the following shakers listed in Table 8.

Table 7 Spectrophotometers


One of the following spectrophotometers:• DTX 880 Multimode Detector, with:

Genomic Filter SlideBeckman Coulter 987921

A30184

SpectraMax High throughput Microplate Spectrophotometer

Molecular Devices

Plus384

Table 8 Shakers

Shaker Supplier Cat. No.

Digital Microplate Shaker Thermo Scientific 88880023 or 88880024

Jitterbug™ Boekel Scientific Model 130 000



Plate centrifuge One plate centrifuge is required for the Axiom™ 2.0 Assay 384 Samples Workflow. We recommend the plate centrifuges listed in Table 9. When centrifuging and drying pellets, the centrifuge must be able to spin down plates at:

• rcf: 3200 xg with an appropriate rotor - bucket combination (4000 RPM for the Eppendorf 5810R configuration described below)

• temperature: 4°C

In addition, the bottom of the rotor buckets should be soft rubber to ensure that the deep well plates do not crack. Do not use buckets where the plates sit directly on a metal or hard plastic bottom. For the Eppendorf 5810R, do not use the A-4-62 rotor with a WO-15 plate carrier (hard bottom).

Relative centrifugal force (rcf) can be calculated as follows:

rcf = (1.118 × 10-5) R S2

where R is the radius of the rotor in centimeters, and S is the speed of the centrifuge in revolutions per minute.

Table 9 Plate centrifuges recommended for the Axiom™ 2.0 Assay for 384HT Samples Automated Workflow


One of the following centrifuges:

• Allegra® 25R Refrigerated Benchtop Centrifuge Beckman Coulter 369434 (60 Hz, 280 V)369435 (50/60 Hz, 200 V)369436 (50 Hz, 230 V)

368954 S5700 Microplate rotor

• Centrifuge 5810R (refrigerated)

– A-4-81 MTP/Flex swinging bucket rotor with 4 microtest-plate buckets

Eppendorf 022625501 (60 Hz, 120 V)022625101 (50 Hz, 120 V, 20 AMP version)022625551 (50 Hz, 230 V)

022638807

• Sorvall® Legend® XTR (refrigerated), with: Thermo Scientific 75004521 (60 Hz, 120 V)75004520 (50 Hz, 230 V)75004523 (50/60 Hz, 230 V USA and Canada)

TX-750 high visibility swinging rotor bucket 75003607

Carrier for microplates (including plate trays and neoprene pads)

One of either:• Set of two carriers (75003795)• Set of four carriers (75003617)


Chapter 2 Equipment and supplies requiredOther equipment, consumables, and reagents required 2

Other common lab equipment required

Other reagents and gels required

Table 10 Other equipment required


Freezer, –20°C Any vendor —

Refrigerator, 2 to 8°C Any vendor —

Vortex-Genie® (for plates and microtubes)1

1 Equivalent items from other manufacturers are acceptable.

Scientific Industries

SI-0236 (120 V/60 Hz)SI-0246 (230 V/50 Hz)

Mini Microcentrifuge, for 2 mL tubes1 VWR 93000-196 (120V)93000-196 (230V)

Bel-Art Cryo-Safe Mini Cooler, –15°C1 VWR 47751-730

Ice bucket, 4 to 9 liters Any vendor —

Table 11 Other Reagents Required


2-Propanol, anhydrous, 99.5% (Isopropanol) Sigma-Aldrich 278475

Reduced EDTA TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA)

Thermo Fisher Scientific

75793

Table 12 Reagents and Gels Required to Run QC Steps


Mother E-Base™ Device

Thermo Fisher Scientific

EB-M03

Daughter E-Base™ Device EB-D03

E-Gel® 48 4% agarose gels (for Axiom QC) G8008-04

TrackIt™ 25 bp DNA Ladder (for Axiom QC) 10488-022

TrackIt™ Cyan/Orange Loading Buffer (for Axiom QC) 10482-028

E-Gel® 48 1% agarose gels (for gDNA QC) G8008-01

RediLoad™ (for gDNA QC) 750026

E-Gel® 96 High Range DNA Marker (for gDNA QC) 12352-019

Water, nuclease-free, ultrapure MB grade (only required for performing rehybridization protocols and gel QC)

71786



Pipettes and tips Pipettes and tips recommended for performing the gel QC steps in the Axiom™ 2.0 Assay 384 Samples Workflow are listed in Table 13.

Other Consumables Required

Table 13 Pipettes and tips

Item Supplier Cat. No.s

The following single or multichannel pipettes are required: Single Channel Multichannel

Pipette, 0.5–10 μL Rainin L-10 L12-10

Pipette, 2–20 μL Rainin L-20 L12-20

Pipette tips, LTS filter Rainin GP-L10F GP-L10F

Table 14 Consumables Required


Adhesive film for 96-well plates – use one of the following:

• MicroAmp® Clear Adhesive Film Thermo Fisher Scientific

4306311

• Microseal 'B' Film Bio-Rad MSB1001

Kimwipes® Your choice —

Markers, permanent, fine point Your choice —


A Supplier contact list

Table 15 Supplier contact list

Supplier Website Address

Axygen/Corning www.corning.com/lifesciences

Beckman Coulter www.beckmancoulter.com

Bio-Rad www.bio-rad.com

E&K Scientific www.eandkscientific.com

Eppendorf www.eppendorf.com

Molecular Devices www.moleculardevices.com

Rainin www.rainin.com

Scientific Industries www.scientificindustries.com

Sigma-Aldrich www.sigmaaldrich.com

Thermo Fisher Scientific(Thermo Scientific, Applied Biosystems, Invitrogen, Life Technologies, Affymetrix)

www.thermofisher.com

VWR www.vwr.com


http://www.bio-rad.com

http://www.sigma-aldrich.com

http://www.corning.com/lifesciences

http://www.bio-rad.com/

http://www.eandkscientific.com/

http://www.eppendorf.com

http://www.moleculardevices.com

http://www.rainin.com

http://www.scientificindustries.com

http://www.sigmaaldrich.com

http://www.thermofisher.com/

https://www.vwr.com

http://www.beckmancoulter.com

Documentation and support

Related documentation

Table 16 Documents related to the Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP

Document Publication number Description

Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP User Guide

703268 Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP User Guide (Windows XP and 7)

Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Site Preparation Guide

703269 Provides guidance on reagents, instruments, and supplies required to run the Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP.

Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Quick Reference (Windows XP)

703270 An abbreviated reference for the target preparation step of the Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP running on the Windows XP operating system. This quick reference document is intended for experienced users.

Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP Quick Reference (Windows 7)

703371 An abbreviated reference for the target preparation step of the Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP running on the Windows 7 operating system. This quick reference document is intended for experienced users.

Axiom™ 2.0 384HT gDNA Sample Prep Quick Reference

703163 An abbreviated reference on the genomic DNA sample preparation protocol for 384HT-array format.

GeneTitan™ MC Protocol for Axiom™ 384HT Array Plate Processing Quick Reference

703164 An abbreviated reference for processing 384HT-array format plates on the GeneTitan Multi-Channel (MC) Instrument.

GeneTitan™ Multi-Channel Instrument User Guide

08-0308 The GeneTitan Multi-Channel (MC) Instrument automates array processing from target hybridization to data generation by combining a hybridization oven, fluidics processing, and state-of-the art imaging device into a single bench-top instrument. This document detailing the use, care, and maintenance for the GeneTitan MC Instrument.


Documentation and supportRelated documentation

GeneTitan™ Multi-Channel Instrument Site Preparation Guide

08-0305 Provides guidance on creating and maintaining the proper environment required for the GeneTitan Multi-Channel Instrument.

Analysis and software

Axiom™ Genotyping Solution Data Analysis Guide

702961 This guide provides information and instructions for analyzing Axiom genotyping array data. It includes the use of Axiom™ Analysis Suite, Applied Biosystems Microarray Power Tools (formerly APT) and SNPolisher R package to perform quality control analysis (QC) for samples and plates, SNP filtering prior to downstream analysis, and advanced genotyping methods.

Applied Biosystems ™ GeneChip™ Command Console™ Software User Guide

702569 This user guide provides instructions on using Applied Biosystems GeneChip Command Console Software (AGCC) used to control GeneChip instrument systems. Command Console Software provides an intuitive set of tools for instrument control and data management used in the processing of GeneChip Arrays.

Axiom™ Analysis Suite User Guide 703307 This user guide provides instructions on using Axiom™ Analysis Suite—a single-source software package to enable complete genotyping analysis of all Axiom arrays.

Other

Biomek® Liquid Handler User’s Manual 987834 This document is installed at the same time as the Biomek FXP Target Prep Express software. To access, click Start All Programs Beckman Coulter Manuals.

Biomek® Software User’s Manual B30026AA This document is installed at the same time as the Biomek FXP Target Prep Express software. To access, click Start All Programs Beckman Coulter Manuals.

Symbol® Cyclone™ M2000 Series Product Reference Guide

72E-39696-06 Barcode scanners documentation from manufacturer.

Table 16 Documents related to the Axiom™ 2.0 Assay 384HT-Array Format Automated Protocol for Beckman Biomek FXP

Document Publication number Description


Documentation and supportCustomer and technical 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

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• Order and web support

• Product documentation, including:

– User guides, manuals, and protocols

– Certificates of Analysis

– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers, contact the manufacturer.

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 www.thermofisher.com/us/en/home/global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at thermofisher.com/support.


http://thermofisher.com/support

http://www.thermofisher.com/us/en/home/global/terms-and-conditions.html

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5 December 2017


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