Thermo Fisher Scientific GeneChip HT Pico Kit Assay Automated Workflow User guide

Brand: Thermo Fisher Scientific

Model: GeneChip HT Pico Kit Assay Automated Workflow

Type: User guide

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

GeneChip™ HT Pico Kit Assay Automated

Workﬂow

SITE PREPARATION GUIDE

for use with:

GeneChip™ Expression Arrays

GeneChip™ HT Pico Kit

Beckman Coulter™ Biomek™ FXP Target Prep Express Automated Workstation

Catalog Numbers 902790 and 902791

Publication Number MAN0018105

Revision B.0

Manufacturer:

Thermo Fisher Scientiﬁc Baltics UAB |

V.A. Graiciuno 8, LT-02241 |

Vilnius, Lithuania

Products:

GeneChip™ HT Pico Kit

Manufacturer:

Aymetrix Pte Ltd |

7 Gul Circle #2M-01 |

Keppel Logistics Building |

Singapore 629563

Products:

GeneChip™ expression arrays

For descriptions of symbols on product labels or product documents, go to thermoﬁsher.com/symbols-deﬁnition.

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

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. 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. MAN0018105

Revision Date Description

B.0 09 October 2020 Added additional Bio-Rad Hard Shell PCR Plate catalog number.

A.0 27 December 2018 •Initial release in Thermo Fisher Scientiﬁc document control system.

•Supersedes legacy Aymetrix publication number 703399.

•Updated to the current document template, with associated

updates to trademarks, logos, licensing, and warranty.

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.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Contents

■CHAPTER 1 Biomek™ FXP Target Prep Express Automated

Workstation conﬁguration .......................................................... 4

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

Instrument speciﬁcations and settings ............................................. 6

Other equipment required ....................................................... 10

Thermal cyclers ........................................................... 10

Spectrophotometer ........................................................ 10

Miscellaneous equipment required ........................................... 10

■CHAPTER 2 Materials required and GeneChip™ HT Pico v1.0

method installation ................................................................ 11

Part 1: Equipment, reagents, consumables, and labware required .................... 11

Equipment ................................................................ 11

Reagents ................................................................. 13

Consumables and labware .................................................. 15

Labware templates ......................................................... 21

Part 2: Biomek™ HT Pico v1.0 method installation .................................. 23

Time requirements ......................................................... 23

Install the method ﬁles ..................................................... 24

Import the method into the Biomek™ FXP Target Prep Express

Automated Workstation .................................................. 26

Make required edits to Biomek™ Software v4.1.41 (Build 41) .................... 30

Import and conﬁgure the Biometra T-Robot thermal cycler program .............. 34

Set Microsoft™ Excel™ 2010 options ......................................... 40

Validate the method ........................................................ 40

Error recovery ............................................................. 41

Test the method with a water run ............................................ 42

■Documentation and support ....................................................... 47

Related documentation ......................................................... 47

Customer and technical support ................................................. 48

Limited product warranty ........................................................ 48

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP3

Biomek™ FXP Target Prep

Express Automated Workstation

conﬁguration

■Equipment ............................................................................ 4

■Instrument speciﬁcations and settings ................................................... 6

■Other equipment required ............................................................. 10

Equipment

The Beckman Coulter™ Biomek™ FXP Target Prep Express Automated Workstation is required to run

GeneChip™ High Throughput (HT) expression assays. This system includes the accessories, software,

and deck conﬁguration listed in Table 1 and displayed in Figure 1. For information on upgrading a

Biomek™ liquid handler already at your site, contact Beckman Coulter™ Inc. Chapter 2, “Materials

required and GeneChip™ HT Pico v1.0 method installation” lists the components required to run the

GeneChip™ HT Pico Kit Assay Automated Workﬂow.

Unless otherwise indicated, all materials are available through thermoﬁsher.com. "MLS" indicates that

the material is available from ﬁsherscientiﬁc.com or another major laboratory supplier.

Table 1 Biomek™ FXP Target Prep Express Automated Workstation components required for running

GeneChip™ HT methods for expression.

Item Quantity

Beckman

Coulter™

Cat. No.

Biomek™ FXP Target Prep Express Automated Workstation

The part number for this workstation includes the components listed below:

1 A83103

•Biomek™ FXP Dual Multichannel Span-8 1 A31844

•Biomek™ Win 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

4GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Table 1 Biomek FXP Target Prep Express Automated Workstation components required for running

GeneChip HT methods for expression. (continued)

Item Quantity

Beckman

Coulter™

Cat. No.

•Pkg Static ALP Platform 4 719357

•4 × 3 ALP Kit 1 719948

•Static Peltier ALP 1 A93938

•Shaking Peltier ALP 1 A93942

•Deep well plate adapter (required for Axiom™ assays) 1 A83050

•Thin PCR adapter (required for expression assays) 1 A19709

•Frame for Modular Reservoirs 3 372795

•24-Position Tube Rack Holder 1 373661

•11-mm Diameter Tube Rack Inserts (case of 25) 1 373696

•Blue Heater/Chiller 24-well Block

(referred to as Reagent Cold Block in this document)

1 A83054

•Biometra T-Robot Integration - v4.1 1 969125

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Equipment 1

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP5

Instrument speciﬁcations and settings

To perform GeneChip™ HT Pico expression assays successfully on the Biomek™ FXP Target Prep

Express Automated Workstation 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 (Pod 1) and Span-8 head right pod (Pod 2)

–1-mL syringes and low-volume tubing on the Span-8 system

–Thin PCR adapter mounted on the Shaking Peltier Device

–Shaking Peltier ALP Labware Guides properly adjusted

–ALPs secured to deck. See Figure 1.

•Degassed water as system ﬂuid

•Clean compressed air at 40–80 psi

•Computer workstation speciﬁcations:

–Microsoft™ Windows™ 7 operating system

–Internet Explorer™ v8.0

–Microsoft™ Excel™ 2010 (must be 32‑bit version)

–Biomek™ Software v4.1.31 (Build 31) or v4.1.41 (Build 41)

•Biomek™ Software conﬁguration:

–Ensure that the Aymetrix™ deck is the default deck.

–Ensure that deck location SPelt96_1 has the device ShakingPeltier1 associated with it.

–Ensure that deck location Pelt_1 has the device StaticPeltier1 associated with it.

–Ensure that deck location TR1 is ALP type Span8TrashRight (not Span8TipTrashRight).

•Check for a properly framed deck for the Biomek™ 200-µL 96-Channel Disposable Pipetting Head

and the Biomek™ Span-8 Waste ALP pods.

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

–If the deck needs to be reframed, save a current copy of the instrument ﬁle for backup.

–Exit and restart the Biomek™ Software after installing the Aymetrix™ deck and after any

changes in deck framing. This saves the new values in the default instrument (.bif) ﬁle.

•Additional pod settings:

–Navigate to Instrument4Hardware Setup4Pod24Additional Pod Settings.

–Pod 2 (Span-8) settings (Figure 2)

Set System Trailing Airgap to 20 µL.

–Navigate to Instrument4Hardware Setup4Pod14Additional Pod Settings.

–Pod 1 (MC96) settings (Figure 3)

Check Always move to Z-Max when roving box.

Set the Additional Roving Height ﬁeld to 0.45 cm or less (default is 0.75 cm).

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Instrument speciﬁcations and settings

6GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

•Set the adjustable labware corner guides on the Shaking Peltier ALP:

–Ensure that the thin adapter plate is installed on the peltier, if not, install the thin adapter plate.

–To adjust the newer (tan) adjustable corner guides the Shaking Peltier ALP must be removed

from the deck to allow access to the rear screws; to adjust the older (blue) adjustable corner

guides the shaking peltier can remain on the deck.

–The tan adjustable corner guides have 2 ﬂathead screws present on each of the outer sides

of the four guides to perform adjustments to hold labware; the blue adjustable corner guides

have 2 hex screws on the top of each corner guide to perform adjustments to hold labware

–Place a Costar Polystyrene 96-Well U-bottom Plate onto the Shaking Peltier ALP

–Tan adjustable corner guides: tighten the ﬂat head screws on the sides of each labware guide

(8 total screws) until a slight resistance is felt. Then tighten each screw an additional 1/2 turn.

–Blue adjustable corner guides: adjust the corner guide screws until labware is held snugly.

–Ensure that the Costar Polystyrene 96-Well U-bottom Plate is held snugly but can be removed

from the Shaking Peltier ALP.

–Ensure that a Bio-Rad™ Hard-Shell™ 96-Well PCR Plate plate can be placed into and removed

from the Shaking Peltier ALP.

–Reinstall the Shaking Peltier ALP on the deck and reframe the position for Pod 1 if necessary.

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Instrument speciﬁcations and settings 1

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP7

Figure 1 Biomek™ FXP Target Prep Express Automated Workstation system (top) and deck conﬁguration

(bottom).

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Instrument speciﬁcations and settings

8GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Figure 2 Hardware setup changes for the span-8 ALP on Pod 2.

Figure 3 Hardware setup changes for the 96-channel head on Pod1.

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Instrument speciﬁcations and settings 1

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP9

Other equipment required

Thermal cyclers

The GeneChip™ HT Pico v1.0 method has 2 thermal cycler options for reaction incubations: an on-deck

Biometra™ TRobot 96 Thermocycler or an o-deck thermal cycler.

For on-deck incubation using a Biometra™ TRobot 96 Thermocycler (Biometra™ Cat. No. 050-991), the

thermal cycler should be purchased directly from a local Biometra™ distributor. For information, see

analytikjena.com. The Biometra™ TRobot 96 Thermocycler integration solution must be purchased

separately from Beckman Coulter™.

To use an o-deck thermal cycler, ensure that the thermal cycler can accept the full-skirted Bio-Rad

Hard-Shell 96 PCR plate. If the hybridization-ready target will be prepared for cartridge arrays, ensure

that the thermal cycler can accept FrameStar™ Break-A-Way PCR Plates. See Table 9.

Spectrophotometer

The GeneChip™ HT Pico v1.0 method has 2 options for measuring nucleic acid concentration: a UV/Vis

plate reader or a NanoDrop™ spectrophotometer (or equivalent instrument). NanoDrop™ instruments can

be purchased from Thermo Fisher Scientiﬁc. There are no unique plate reader requirements except that

the plate reader must accommodate Greiner UV-Star plates. See Table 9.

Miscellaneous equipment required

"MLS" indicates that the material is available from ﬁsherscientiﬁc.com or another major laboratory

supplier.

Table 2 Other equipment required

Item Source

Benchtop cooler, –20°C MLS

Centrifuge for 96-well plates and 1.5-mL and 2.0-mL tubes MLS

Freezer, –20°C, not frost-free MLS

Ice bucket MLS

Pipette with pipette tips MLS

Refrigerator, 2–8°C MLS

Vortex mixer MLS

Chapter 1 Biomek™ FXP Target Prep Express Automated Workstation conﬁguration

Other equipment required

10 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Materials required and GeneChip™

HT Pico v1.0 method installation

■Part 1: Equipment, reagents, consumables, and labware required .......................... 11

■Part 2: Biomek™ HT Pico v1.0 method installation ........................................ 23

“Part 1: Equipment, reagents, consumables, and labware required” on page 11 of this chapter lists

the part numbers and suppliers for the equipment, reagents, consumables, and labware that have been

veriﬁed for use with the GeneChip™ HT Pico Kit on the Beckman Coulter™ Biomek™ FXP Target Prep

Express Automated Workstation. “Part 2: Biomek™ HT Pico v1.0 method installation” on page 23 of

this chapter provides detailed instructions for the installation and validation of the HT Pico v1.0 method

for the Biomek™ FXP Target Prep Express Automated Workstation.

Part 1: Equipment, reagents, consumables, and labware

required

Unless otherwise indicated, all materials are available through thermoﬁsher.com. "MLS" indicates that

the material is available from ﬁsherscientiﬁc.com or another major laboratory supplier.

Equipment

Unless otherwise indicated, all materials are available through thermoﬁsher.com. "MLS" indicates that

the material is available from ﬁsherscientiﬁc.com or another major laboratory supplier.

Table 3 Equipment required for target preparation.

Quantity Item Source

1 Biomek™ FXP Target Prep Express Automated Workstation Beckman Coulter™

A83103

1 24-Position Tube Rack Holder Beckman Coulter™

373661

11-mm Diameter Tube Rack Inserts (11 mm, white, case of 25) Beckman Coulter™

373696

1 Reagent Cold Block, 24 Well Block Beckman Coulter™

A83054

1 Thin PCR adapter (installed on the Shaking Peltier ALP) Beckman Coulter™

A19709

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP11

Table 3 Equipment required for target preparation. (continued)

Quantity Item Source

1 Centrifuge (for tube and plate) MLS

1 Pipettes MLS

1 Spectrophotometer (plate, single channel, or multichannel) MLS

1 Thermal cycler (for optional o-deck incubation) MLS

needed

Adhesive PCR plate seals (for optional o-deck incubation) MLS

1 Vortex mixer MLS

Table 4 Expression installation kits required for the HT Pico method.

Quantity Item Source

1 GeneChip™ HT 3' IVT PLUS and WT PLUS Core Installation Kit ,

components:

•Alpaqua™ Magnetic Plate

•Alpillo™ Plate Cushion

•Arched auto-sealing lids with wide tabs (package of 4)

902453

1 GeneChip™ HT Pico Installation Kit, components:

•HT Pico reagent cold block template

•HT Pico reservoir frame stickers

•PCR tube holder

902901

HT Pico v1.0 Biomek™ method ﬁle and support ﬁles 600757

(Installed by Thermo

Fisher Scientiﬁc FAS)

Table 5 Equipment required for array processing.

Item Source

GeneChip™ System for Cartridge Arrays

•GeneChip™ Hybridization Oven 645

•GeneChip™ Fluidics Station 450

•GeneChip™ Scanner 3000 7G System

•00-0331 (110/220V)

•00-0079

•00-0213

GeneChip™ AutoLoader with External Barcode Reader 00-0090 (GCS 3000 7G S/N 501)

00-0129 (GCS 3000 7G S/N 502)

GeneTitan™ Multi-Channel (MC) Instrument Contact Thermo Fisher Scientiﬁc

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required

12 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Reagents

Unless otherwise indicated, all materials are available through thermoﬁsher.com. "MLS" indicates that

the material is available from ﬁsherscientiﬁc.com or another major laboratory supplier.

Table 6 Contents and storage: GeneChip™ 3′ IVT Pico Kit (Cat. No. 902790, 30 reactions) and

GeneChip™ HT Pico Kit (Cat. No. 902791, 96 reactions).

Component Storage

Pico Ampliﬁcation Kit, Module 1: cRNA Step

Pico First-Strand Enzyme

–20°C

Pico First-Strand Buer

Pico Cleanup Reagent

Pico 3’ Adaptor Enzyme

Pico 3’ Adaptor Buer

Pico PCR Enzyme

Pico PCR Buer

Pico IVT Enzyme

Pico IVT Buer

Poly-A Control Stock

Nuclease-free Water Any temperature[1]

Pico Ampliﬁcation Kit, Module 2: cDNA Step

Pico 2nd-Cycle Primers

–20°C

Pico 2nd-Cycle ds-cDNA Enzyme

Pico 2nd-Cycle ds-cDNA Buer

Pico Frag. & Label Enzyme

Pico Frag. & Label Buer

Pico Ampliﬁcation Kit, Module 3

Puriﬁcation Beads

4°C[2]

Pico Hydrolysis Buer

Pico Neutralization Buer

Control HeLa RNA

Control RNA (100 ng/μL HeLa total RNA) –20°C

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required 2

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP13

Table 6 Contents and storage: GeneChip 3′ IVT Pico Kit (Cat. No. 902790, 30 reactions) and

GeneChip HT Pico Kit (Cat. No. 902791, 96 reactions). (continued)

Component Storage

GeneChip™ Hybridization Control Kit

20X Hybridization Controls

–20°C

3 nM Control Oligo B2

Tubes Organizer: Plastic vinyl template for organization and storage of components in 9 x 9 array, 81-

places square wells, 5 1/4 in. x 5 1/4 in (for example, Nalgene™ Polycarbonate 9 x 9 CryoBox, Cat. No.

5026-0909 ).

[1] Store the Nuclease-free Water at –20°C, 4°C, or room temperature.

[2] Do not freeze.

Table 7 Additional reagents required.

Item Source

GeneChip™ Hybridization, Wash, and Stain Kit (30 reactions, for cartridge arrays) 900720

GeneTitan™ Hybridization, Wash, and Stain Kit for WT Array Plates (96 reactions) 901622

GeneTitan™ Hybridization, Wash, and Stain Kit for 3’ IVT Arrays (96 reactions) 901530

DNAZap™ PCR DNA Degradation Solutions AM9890

RNaseZap™ RNase Decontamination Solution AM9780

Nuclease-free Water (for elution, dilution and preparing 80% Ethanol Wash Solution):

•~45 mL for 1 × 24 reactions, and

•~120 mL for 1 × 96 reactions

MLS

100% Ethanol (molecular biology grade or equivalent) for preparing 80% Ethanol

Wash Solution:

•~20 mL for 1 × 24 reactions, and

•~50 mL for 1 × 96 reactions

MLS

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required

14 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Consumables and labware

Unless otherwise indicated, all materials are available through thermoﬁsher.com. "MLS" indicates that

the material is available from ﬁsherscientiﬁc.com or another major laboratory supplier.

Thermo Fisher Scientiﬁc does not oer a consumables kit speciﬁcally for use with the HT Pico v1.0

method. The HT WT PLUS Consumables for Biomek™ FXP Target Prep Express (Cat. No. 902508),

when supplemented with 2 additional Bio-Rad™ 'P' pads (Cat. No. MSL2032 ), is sucient to perform 4

complete HT Pico assays for cartridge arrays or 3′ IVT array plates.

When supplemented with 2 additionalBio-Rad™ 'P' pads and 4 additional Bio-Rad Hard-Shell PCR

plate, clear well (Cat. No. HSP9631 or HSP9601), the kit will be sucient to perform 4 complete HT

Pico assays for WT or Clariom™ S array plates.

Table 8 Beckman Coulter™ tips and labware required for 1 full run of the GeneChip™ HT Pico Kit on the

Biomek™ FXP Target Prep Express Automated Workstation.

Item Packaging Total 24X Total 96X Source

Biomek™ P50 Sterile Filtered Tips (magenta

box)[1]

96/box

10 boxes/case

12 boxes 14 boxes Beckman

Coulter™

A21586

Biomek™ P250 Sterile Filtered Tips (aqua

box), for AP96 multichannel pipettor

•Plates

•Cartridges

96/box

10 boxes/case

•6 boxes

•5 boxes

•6 boxes

•5 boxes

Beckman

Coulter™

717253

Biomek™ P250 Span-8 Sterile Filtered

Tips(green box), for span-8 pipettor

96/box

10 boxes/case

1 box 2 boxes Beckman

Coulter™

379503

Biomek™ P1000 Span-8 Conductive Sterile

Filtered Tips (yellow box) or Biomek™ P1000

Span-8 Nonconductive Sterile Filtered Tips

(orange box), for span-8 pipettor[2]

96/box

5 boxes/case

2 boxes 2 boxes Beckman

Coulter™

987925 or

B01124

Quarter Reservoir, Divided by Width, 19 mL

per section

•Plates

•Cartridges

48 units/case

•6 units

•4 units

•6 units

•4 units

Beckman

Coulter™

372792

Quarter Reservoir, 40 mL

•Plates

•Cartridges

48 units/case

•5 units

•4 units

•5 units

•4 units

Beckman

Coulter™

372790

Frame for Modular Reservoirs 1 3 reusable

frames

3 reusable

frames

Beckman

Coulter™

372795

[1] Two fewer boxes of this tip required for NanoDrop™ quantification option for method parts 2 and 4.

[2] The HT Pico v1.0 method can use conductive and nonconductive P1000 Span-8 tips interchangeably.

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required 2

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP15

Table 9 Consumables and labware used on the Biomek™ FXP Target Prep Express Automated Workstation

deck.

Item Source Image

Biomek™ P50 Sterile Filtered Tips

(magenta box)

Beckman Coulter™ A21586

Biomek™ P250 Sterile Filtered Tips

(aqua box)

Beckman Coulter™ 717253

Biomek™ P250 Span-8 Sterile

Filtered Tips(green box)

Beckman Coulter™ 379503

Biomek™ P1000 Span-8 Conductive

Sterile Filtered Tips (yellow

box) or Biomek™ P1000 Span-8

Nonconductive Sterile Filtered Tips

(orange box)

Beckman Coulter™

987925 (yellow) or

B01124 (orange)

Reservoir, Quarter

•Quarter Reservoir, 40 mL

•Quarter Reservoir, Divided by

Width, 19 mL per section

Beckman Coulter™

•372790

•372792

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required

16 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Table 9 Consumables and labware used on the Biomek FXP Target Prep Express Automated Workstation

deck. (continued)

Item Source Image

Frame for Modular Reservoirs

(3 total needed for HT Pico Method,

reusable for subsequent runs)

Beckman Coulter™ 372795

96-well deep well microplate,

polypropylene, 2 mL, non-sterile

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

(or Fisher Scientiﬁc™ AB0932 )

Greiner U-bottom (round) plate,

polypropylene

Used as a distribution plate for

cartridge hybridization mix and is not

interchangeable with the polystyrene

U-bottom plate.

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

(or Fisher Scientiﬁc™ 07-000-146)

Bio-Rad Hard-Shell PCR plate, clear

well

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

Note: One additional plate per run

required for WT or Clariom™ S array

plate option.

(or Bio-Rad™HSP9631 or HSP9601 )

Greiner UV-Star plate, nonsterile,

clear, ﬂat bottom

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

(or Fisher Scientiﬁc™ 07-000-407)

Costar 96-Well U-bottom plate,

polystyrene

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required 2

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP17

Table 9 Consumables and labware used on the Biomek FXP Target Prep Express Automated Workstation

deck. (continued)

Item Source Image

24-well plate, 10 mL, square well,

pyramid bottom, polypropylene

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

(or Seahorse Bioscience S30024)

'P' Pad for lid, autosealing

microplates, arched with Microseal

Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

Note: One new 'P' Pad is required

per run for HT Pico.

(or Bio-Rad™ MSP1003, MSL2032

with lid)

FrameStar Break-A-Way plate Included in GeneChip™ HT WT

PLUS Consumables for Biomek™

FXP Target Prep Express Automated

Workstation, 902508

(or Thomas Scientiﬁc 4ti-1000/B)

Nalgene™ Polycarbonate 9 x 9

CryoBox

5026-0909

Alpaqua™ Magnetic Plate Included in GeneChip™ HT 3' IVT

PLUS and WT PLUS Core Installation

Kit , 902453

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required

18 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

Table 9 Consumables and labware used on the Biomek FXP Target Prep Express Automated Workstation

deck. (continued)

Item Source Image

Alpillo™ Plate Cushion Included in GeneChip™ HT 3' IVT

PLUS and WT PLUS Core Installation

Kit , 902453

Arched auto-sealing lids with wide

tabs

Included in GeneChip™ HT 3' IVT

PLUS and WT PLUS Core Installation

Kit , 902453

Blue Heater/Chiller 24-well Block

Block must be chilled to 4°C before

use.

Beckman Coulter™ A83054

HT Pico Cold Block Template

The template is designed for the

GeneChip™ HT Pico Kit and ﬁts

precisely onto the reagent cold

block. The cold block template helps

ensure proper placement of reagent

tubes into the block for each part of

the assay.

Included in the GeneChip™ HT Pico

Installation Kit, 902901.

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required 2

GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP19

Table 9 Consumables and labware used on the Biomek FXP Target Prep Express Automated Workstation

deck. (continued)

Item Source Image

HT Pico Reservoir Frame Stickers

Place modular reservoir template

stickers on the front of the modular

reservoir frames to ensure proper

placement of modular reservoirs and

reagents.

Included in the GeneChip™ HT Pico

Installation Kit, 902901.

PCR Tube Holder

For use with FrameStar™ Break-A-

Way PCR Plate in cartridge array

hybridization setup.

Included in the GeneChip™ HT Pico

Installation Kit, 902901.

(or Bio-Rad™ TRC-9601)

24-Position Tube Rack Holder with

11-mm Diameter Tube Rack Inserts

Beckman Coulter™

373661 (rack)

373696 (inserts)

Thin PCR Adapter

This adapter is typically installed

on the Shaking Peltier ALP by

a Beckman Coulter™ ﬁeld service

technician during new system

installation or a system upgrade.

Ensure that you have the thin PCR

adapter installed on the Shaking

Peltier ALP prior to running this

assay.

Beckman Coulter™ A19709

GeneTitan™ Hybridization Tray Part. No. 500867

(GeneTitan™ trays and lids are

provided with the array plate when

ordered. The part number provided

here is for identiﬁcation purposes

only.)

Chapter 2 Materials required and GeneChip™ HT Pico v1.0 method installation

Part 1: Equipment, reagents, consumables, and labware required

20 GeneChip™ HT Pico Kit Assay Automated Workﬂow Site Preparation Guide—Biomek™ FXP

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Thermo Fisher Scientific GeneChip HT Pico Kit Assay Automated Workflow User guide

Thermo Fisher Scientific GeneChip HT Pico Kit Assay Automated Workflow User guide

Thermo Fisher Scientific GeneChip HT Pico Kit Assay Automated Workflow User guide

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