OpenArray AccuFill System User Guide (PN 4456986A)

OpenArray® AccuFill™ System
User Guide
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
This user guide is the proprietary material of Applied Biosystems, LLC or its affiliates and is protected by laws of copyright. The customer of the OpenArray®
AccuFill™ is hereby granted limited, non-exclusive rights to use this user guide solely for the purpose of operating the OpenArray® AccuFill™ System.
Unauthorized copying, renting, modifying, or creating derivatives of this user guide is prohibited.
Information in this document is subject to change without notice.
NOTICE TO PURCHASER: Limited Licenses
The OpenArray® AccuFill™ system as well as methods and systems involving the same are covered by US Patent No. 7,547,556, and corresponding claims
in any foreign counterpart patents thereof. No right is conveyed expressly, by implication, or by estoppel under any other patent claim, such as claims to
apparatus, reagents, kits, or methods such as 5' nuclease methods, other than device claims covering the purchased product. Further information on
purchasing licenses may be obtained from the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
WARRANTIES
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO
THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED
BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL,
INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT
LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
TRADEMARKS
The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.
Excel® and Windows® are trademarks of Microsoft Corporation.
Pluronic is a trademark of BASF Corporation. LightCycler is a trademark of Roche Diagnostics. TaqMan is a registered trademark of Roche Molecular Systems,
Inc.
© Copyright 2010, Life Technologies Corporation. All rights reserved.
Part Number 4456986 Rev. A
06/2010
Contents
About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Safety information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Safety alert words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Safety labels on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
CHAPTER 1
Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR run . . . . . . . . . . . . . . . . . . . 10
Materials and equipment required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Prepare the reagents for use in the master mix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Sample plate preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Prepare sample plate for a TaqMan® OpenArray® Real-Time PCR run . . . . . . . . . . . . . . . . . 13
Materials and equipment required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Sample plate preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Prepare sample plate for a TaqMan® OpenArray® Genotyping run . . . . . . . . . . . . . . . . . . . . . 15
Sample plate preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Prepare the DNA samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Quantity of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Quantification procedure for human DNA samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Perform multi-sample loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
CHAPTER 2
Sample Loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Materials and equipment required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Important guidelines for handling the plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Initialize the system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Prepare the cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Prepare for loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Load an OpenArray plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Load an OpenArray plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Loading history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
OpenArray® AccuFill™ System User Guide
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Contents
CHAPTER 3
Sample Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Use Sample Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
CHAPTER 4
Prepare the plate for the NT Cycler . . . . . . . . . . . . . . . . . . . . . . . . . 41
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Insert the loaded OpenArray® plate into a case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Seal the OpenArray® plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Frame the case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
CHAPTER 5
OpenArray® AccuFill™ Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
The File menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Create Template Sample Plate File Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Explore OpenArray Plate File Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Explore Sample Plate File Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Explore Loaded OpenArray Plate File Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
50
50
50
50
The Instrument menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Setup and Load OpenArray Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cancel Current Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Show Deck . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Show Loading History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Show Instrument Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Run System Self Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Edit Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
51
51
51
51
51
52
52
52
Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
APPENDIX A
Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
How to order from the Applied Biosystems website . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Required equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Required equipment and materials not included . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Optional materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Required reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Required consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
APPENDIX B
System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
OpenArray® AccuFill™ System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Available run types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4
OpenArray® AccuFill™ System User Guide
Contents
APPENDIX C
Cleaning the OpenArray® AccuFill™ instrument . . . . . . . . . . . . . . . 63
Cleaning instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Clean the outside of the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Clean the inside of the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Spill accidents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
APPENDIX D
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Instrumentation safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Symbols on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Locations of safety labels on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
General instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Physical hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Workstation safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . 71
Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
General chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Chemical waste safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Safety alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
General alerts for all chemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Specific alerts for instrumentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Documentation and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Obtaining support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
OpenArray® AccuFill™ System User Guide
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Contents
6
OpenArray® AccuFill™ System User Guide
About This Guide
Purpose
The OpenArray® AccuFill™ System User Guide provides reference information for
the OpenArray AccuFill system and describes how to prepare, maintain, and
troubleshoot the system.
Safety information
Note: For general safety information, see this section and Appendix D, “Safety”
on page 65. When a hazard symbol and hazard type appear by a chemical name
or instrument hazard, see the “Safety” Appendix for the complete alert on the
chemical or instrument.
Safety alert words
Four safety alert words appear in Applied Biosystems user documentation at points in
the document where you need to be aware of relevant hazards. Each alert word—
IMPORTANT, CAUTION, WARNING, DANGER—implies a particular level of
observation or action, as defined below:
IMPORTANT! – Indicates information that is necessary for proper instrument
operation, accurate chemistry kit use, or safe use of a chemical.
CAUTION! – Indicates a potentially hazardous situation that, if not avoided,
may result in minor or moderate injury. It may also be used to alert against
unsafe practices.
WARNING! – Indicates a potentially hazardous situation that, if not avoided,
could result in death or serious injury.
DANGER! – Indicates an imminently hazardous situation that, if not avoided,
will result in death or serious injury. This signal word is to be limited to the
most extreme situations.
Except for IMPORTANTs, each safety alert word in an Applied Biosystems document
appears with an open triangle figure that contains a hazard symbol. These hazard
symbols are identical to the hazard symbols that are affixed to Applied Biosystems instruments
(see “Safety symbols” on page 66).
OpenArray® AccuFill™ System User Guide
7
About This Guide
Safety information
SDSs
The Safety Data Sheets (SDSs) for any chemicals supplied by Applied Biosystems or
Ambion are available to you free 24 hours a day. For instructions on obtaining SDSs,
see “SDSs” on page 73.
IMPORTANT! For the SDSs of chemicals not distributed by Applied Biosystems
or Ambion contact the chemical manufacturer.
Safety labels on instruments
The following CAUTION, WARNING, and DANGER statements may be displayed on
Applied Biosystems instruments in combination with the safety symbols described in
the preceding section.
Hazard
symbol
8
English
Français
CAUTION! Hazardous chemicals. Read the Safety
Data Sheets (SDSs) before handling.
ATTENTION! Produits chimiques dangereux. Lire
fiche technique associée au produit avant toute
manipulation.
CAUTION! Hazardous waste. Refer to SDS(s) and
local regulations for handling and disposal.
ATTENTION! Déchets dangereux. Lire fiche
technique associée et prendre connaissance de la
régulation locale associées à la manipulation et
l’élimination des déchets.
DANGER! High voltage.
DANGER! Haute tension.
WARNING! To reduce the chance of electrical
shock, do not remove covers that require tool access.
No user-serviceable parts are inside. Refer servicing
to Applied Biosystems qualified service personnel.
AVERTISSEMENT! Pour éviter les risques
d’électrocution, ne pas retirer les capots dont
l’ouverture nécessite l’utilisation d’outils.
L’instrument ne contient aucune pièce réparable par
l’utilisateur. Toute intervention doit être effectuée par
le personnel de service qualifié venant de chez
Applied Biosystems.
OpenArray® AccuFill™ System User Guide
CHAPTER 1
Sample Preparation
1
This chapter covers:
■
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR run . . . . . . . . . 10
■
Prepare sample plate for a TaqMan® OpenArray® Real-Time PCR run . . . . . . . 13
■
Prepare sample plate for a TaqMan® OpenArray® Genotyping run . . . . . . . . . . 15
OpenArray® AccuFill™ System User Guide
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1
Chapter 1 Sample Preparation
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR run
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR
run
This section provides instructions on preparing samples for a SYBR® OpenArray®
Real-Time PCR run.
Materials and equipment required
See “Ordering Information” on page 55 for a list of equipment, kits, and consumables
necessary for this procedure.
Prepare the reagents for use in the master mix
To prepare the reagents for use in the master mix:
1. Dilute the concentrated stock of SYBR® Green I dye to 240X shown:
Reagent
Volume in µL
SYBR Green I dye
5
Water
495
Total volume
500
2. Check the stock concentration:
a. Dilute a 10-µL aliquot of diluted SYBR Green I dye into 90 µL water.
b. Measure the optical density at 494 nm.
c. Adjust the OD to 0.5 to 0.6 units by adding SYBR Green I dye or water to the
240X dilution.
d. Store at −20 °C in 20-µL aliquots.
3. Prepare 10 mg/mL BSA working solution as shown. Store at −20 °C in 500 µL
aliquots.
Reagent
Combine
BSA
100 mg
Water
10 mL
Total volume
10 mL at 10 mg/mL
4. Prepare 15% glycerol working solution as shown. Store at room temperature.
Reagent
10
Combine
Glycerol
7.5 mL
Water
42.5 mL
Total volume
50.0 mL at 15%
OpenArray® AccuFill™ System User Guide
Chapter 1 Sample Preparation
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR run
1
Sample plate preparation
To prepare a sample plate for a SYBR OpenArray Real-Time PCR run:
1. Take the vacuum-sealed OpenArray plates out of the freezer and allow them to
thaw for approximately 15 minutes before opening the packages.
2. Prepare Master Mix using the contents of the LightCycler® FastStart DNA Master
kit. The LightCycler® kit comes with four vials labeled 1a, 1b, 2, and 3.
a. Pipette 10 µL of LightCycler FastStart Enzyme from vial 1a to vial 1b.
b. Mix thoroughly by pipetting up and down. Do not use a vortex mixer.
c. Re-label vial 1b with the label “vial 1: Master Mix” provided in the kit or peel
off the label to identify the mix containing the enzyme.
Protect the vial from light.
3. Prepare the OpenArray PCR Master Mix as described in the following table.
Reagent
Volume
(µL)
Stock
Conc.
Final
Conc.
Conc.
Units
LightCycler® DNA Master SYBR®
Green I (prepared in step 2 above)
26.4
10
1.0
X
SYBR® Green
1.1
240
1.0
X
Glycerol
8.8
15
0.5
%
5.3
10
0.2
X
BSA
26.4
10
1.0
mg/mL
MgCl2 (Use a 25-mM solution, i.e.,
vial 2 with a blue cap in the
LightCycler Kit.)
26.4
25
2.5
mM
Formamide
21.1
100
8.0
X
Water
70.9
Pluronic®
F-68
Final volume without sample
—
—
—
186.4
Note: The volumes in this procedure are for one OpenArray plate. If you
are loading more than one OpenArray plate, adjust the total volume.
OpenArray® AccuFill™ System User Guide
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1
Chapter 1 Sample Preparation
Prepare sample plate for a SYBR® OpenArray® Real-Time PCR run
4. Plan which sections of the sample plate you will load with samples. Each
4- x 12-well rectangular area corresponds to one OpenArray plate. You may find
it helpful to mark these areas with a fine point silver marker, as shown in the
following illustration.
2
OpenArray 1
OpenArray
1
Sample
1
A
Sample 1
C
OpenArray 3
OpenArray
3
Sample
1
E
Sample 1
G
OpenArray 5
OpenArray 5
Sample 1
I
Sample 1
OpenArray
7 7
OpenArray
SampleSample
1
1
4
K
M
O
6
1
3
5
7
8
10
12
14
16
18
20
22
24
2
4
6
8
OpenArray 2
OpenArray
Sample
1 2
Sample 1
OpenArray 4
Sample
1 4
OpenArray
Sample 1
OpenArray 6
OpenArray 6
Sample 1
Sample 1
OpenArray
OpenArray 88
Sample
Sample11
5. Pipette 3.5 µL OpenArray PCR Master Mix into each well of the 48-well section of
the 384-well sample plate designated OpenArray 1.
6. Pipette 1.5 µL of the template into each well.
7. Pipette gently up and down to mix. Do not use a vortex mixer.
8. Cover the sample plate with sealing tape. Centrifuge the plate for 1 minute at
1000 rpm.
9. Place the plate on ice to keep the samples cold.
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Real-Time PCR run
1
Prepare sample plate for a TaqMan® OpenArray® Real-Time PCR
run
This section provides instructions on preparing a sample plate for a TaqMan
OpenArray Real-Time PCR run.
Materials and equipment required
See “Ordering Information” on page 55 for a list of equipment, kits, and consumables
necessary for this procedure.
Sample plate preparation
To prepare a sample plate for a TaqMan OpenArray Real-Time PCR run, follow these
steps:
1. Take the vacuum-sealed OpenArray plates out of the freezer and allow them to
thaw for approximately 15 minutes before opening the packages.
2. Prepare the OpenArray PCR Master Mix as described in the tables below.
IMPORTANT! Master Mix components will vary depending on the source of
the template you are using. Use only one of the tables below, depending on
whether your experiment uses cDNA or other DNA.
Reagent for cDNA samples
Volume
(µL)
Stock
Conc.
Final
Conc.
Conc.
Units
GeneAmp® Fast PCR Master Mix
32.0
2
1
X
5X REmix (supplied with the TaqMan
OpenArray kit)
52.8
5
1
X
Water
15.8
—
—
—
Final volume without sample
Reagents for gDNA samples
GeneAmp Fast PCR Master Mix
5X REmix (supplied with the TaqMan
OpenArray kit)
BSA
Water
Final volume without sample
200.6
Volume
(µL)
Stock
Conc.
Final
Conc.
Conc.
Units
132.0
2
1.0
X
52.8
5
1.0
X
1.3
10
0.05
mg/mL
14.5
—
—
—
200.6
Note: The volumes in this procedure are for one OpenArray plate. If you are
loading more than one OpenArray plate, adjust the total volume.
OpenArray® AccuFill™ System User Guide
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Real-Time PCR run
3. Plan which sections of the 384-well sample plate you will load with samples. Each
4- x 12-well, rectangular area corresponds to one OpenArray plate. You may find
it helpful to mark these with a fine point silver marker, as shown in the following
illustration.
2
OpenArray
1 1
OpenArray
1
SampleSample
1
A
C
E
OpenArray
3 3
OpenArray
1
SampleSample
1
OpenArray
5 5
OpenArray
1
SampleSample
1
OpenArray
7 7
OpenArray
1
SampleSample
1
G
I
K
M
O
4
6
8
10
12
14
16
1
3
5
7
18
20
22
2
4
6
8
24
OpenArray
OpenArray 22
Sample 11
Sample
OpenArray
OpenArray 44
Sample 11
Sample
OpenArray
OpenArray 66
Sample 11
Sample
OpenArray
OpenArray 88
Sample 11
Sample
4. Pipette 3.8 µL of Master Mix into each well of the 48-well section of the 384-well
sample plate designated OpenArray plate 1.
5. Pipette 1.2 µL of the sample into each well.
6. Cover the sample plate with sealing tape. Centrifuge the plate for 1 minute at
1,000 rpm. Place the plate on ice to keep the samples cold.
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OpenArray® AccuFill™ System User Guide
Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
1
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
This section provides instructions on preparing a sample plate for a TaqMan
OpenArray Genotyping run.
Sample plate preparation
A single OpenArray plate can accept one to three loads from a sample plate,
depending on how many samples per subarray are required.
To prepare a sample plate for a TaqMan Genotyping run, do the following steps.
Note: For chemical hazard alerts, see Appendix D, Safety.
1. Be sure that the OpenArray 384-well sample plate, OpenArray AccuFill Loader
Tips, and Plate Holder are completely clean and dry:
a. Soak the plate guide, loader tips, and Plate Holder in 10% bleach for at least
10 minutes.
b. Rinse with water, then rinse with ethanol.
c. Let the parts completely air-dry. If they are immediately needed, wipe dry
with paper towels and spray with compressed nitrogen gas.
IMPORTANT! Residual water prevents correct loading of the samples into
the TaqMan OpenArray plates.
2. Fill the appropriate number of TaqMan OpenArray Genotyping Cases with
TaqMan OpenArray Immersion Fluid:
a. Using scissors, open a container of immersion fluid.
b. Place the case in the case rack and fill the case approximately two-thirds with
immersion fluid.
IMPORTANT! Within one hour after opening the container of
immersion fluid, fill the case with immersion fluid, insert a loaded
TaqMan OpenArray plate into the case, then seal the case.
3. Remove the TaqMan OpenArray plates from the freezer, but do not open the
packaging. Allow the TaqMan OpenArray plates to thaw at room temperature
(approximately 5 minutes).
Note: Unopened TaqMan OpenArray plates can remain at room
temperature for up to 24 hours.
IMPORTANT! Thaw only the TaqMan OpenArray plates you will need for
the current loading session.
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
Prepare the DNA samples
Quality of DNA
Be sure that the DNA you use for Genotyping experiments:
• Is extracted from the raw material you are testing with an optimized protocol.
• Does not contain PCR inhibitors.
• Has an A260/230 ratio between 1.7 and 1.9.
• Has an A260/280 ratio between 1.7 and 1.9.
• Is intact as visualized by gel electrophoresis.
• Has not been heated above 60 °C; temperatures above 60 °C can cause
degradation.
Quantity of DNA
Applied Biosystems recommends that you quantify the amount of genomic DNA in
your samples. Note that:
• The TaqMan OpenArray plate requires 250 copies of haploid genome for each
individual through-hole reaction.
• For optimal cluster plot results, it is important to normalize all genomic DNA
samples in an experiment so that each through-hole receives the same input
quantity of sample.
For an example quantification procedure, see the following topic,“Quantification
procedure for human DNA samples”.
Quantification procedure for human DNA samples
The recommended amount of template for each through-hole reaction in a TaqMan
OpenArray plate is 250 copies of the haploid genome, equivalent to 0.84 ng for human
DNA samples. Quantify human DNA samples using the TaqMan RNase P Detection
Reagents Kit and the TaqMan DNA Template Reagents Kit.
Note: The recommended starting concentration for human DNA samples is
50 ng/mL. See the DNA Calculator in the Applied Biosystems TaqMan
OpenArray Genotyping System User Guide (PN4377476 ).
Quantify human
DNA samples
Generate a standard curve using the DNA template standards provided in the TaqMan
DNA Template Reagents Kit and the RNase P gene primers and probe provided in the
TaqMan RNase P Detection Reagents Kit.
Note: Refer to the appropriate instrument user guide for detailed instructions
on performing and analyzing runs.
Note: For chemical hazards alerts, see Appendix D, Safety.
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OpenArray® AccuFill™ System User Guide
Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
1
To quantify human genomic DNA:
1. Create and set up a sequence detector plate document.
2. Prepare the reaction plate using the following components:
• 2✕ TaqMan Universal PCR Master Mix, No AmpErase® UNG
• 20✕ Primer and TaqMan Probe (FAM™ dye) mix
• DNA template standard or genomic DNA sample
• DNase-free, sterile-filtered water
Use at least three replicates of each standard or sample, and use all five DNA
standards to ensure an accurate standard curve is generated. The range of known
copy number should bracket anticipated copy numbers of the unknown samples
on the same reaction plate.
3. Run the reaction plate on an Applied Biosystems Real-Time PCR System using
the following thermal cycling conditions:
AmpliTaq Gold®
enzyme activation
PCR
HOLD
CYCLE (40 cycles)
Denature
Anneal/extend
Time
10 min.
15 sec
1 min.
Temp
95 °C
92 °C
60 °C
4. Generate a standard curve to quantify the amount of DNA in each sample.
The recommended starting concentration for human DNA samples is 50 nanograms
per milliliter. See the DNA Calculator in the Applied Biosystems TaqMan OpenArray
Genotyping System User Guide (PN4377476 ).
Perform multi-sample loading
The OpenArray® AccuFill™ system enables you to load more than one sample per
subarray. Before performing multi-sample loading, set up the sample plates to
accommodate the number of samples you will use per subarray for Genotyping
applications.
The following table shows sample plate volumes, in microliters, for two-sample and
three-sample loads:
Sample PlateVolumes (µL)
Two samples
Three samples
4
3
Note: Multi-sample loading is available only for Genotyping applications.
OpenArray® AccuFill™ System User Guide
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
Set up the sample
plate for two
samples
These instructions describe how to set up a sample plate with two separate DNA
samples.
1. Label the two sections of the sample plate so that you can keep track of what is
loaded in each section. An example is shown in the following illustration.
2
A
OpenArray
1 1
OpenArray
1
Sample Sample
1
C
E
OpenArray
2 2
OpenArray
Sample 1Sample 1
G
I
OpenArray
3 3
OpenArray
Sample 1Sample 1
K
M
OpenArray
4 4
OpenArray
Sample 1Sample 1
O
4
6
8
10
12
14
16
1
3
5
7
18
2
4
6
8
20
22
24
OpenArray11
OpenArray
Sample
Sample22
OpenArray22
OpenArray
Sample22
Sample
OpenArray33
OpenArray
Sample
Sample22
OpenArray44
OpenArray
Sample
Sample22
IMPORTANT! Be sure to track where the samples are in the sample plate.
For each sample you use, Applied Biosystems recommends creating a
sample information file in comma-separated values (CSV) format. This
CSV file can be used in sample integration. See “Use Sample Integration”
on page 39 for more information.
2. Use the following loading arrangement. Refer to the example on page 20 for the
locations of the sample plate sections.
• OpenArray 1 - OpenArray plate for the first run is in Plate Holder position 1.
– The first sample for the subarray comes from section 1 of the sample
plate, which holds samples 1 to 48.
– The second sample for the subarray comes from section 2 of the sample
plate, which holds samples 49 to 96.
• OpenArray 2 - OpenArray plate for the second run is in Plate Holder
position 2.
– The first sample for the subarray comes from section 3 of the sample
plate, which holds samples 1 to 48.
– The second sample for the subarray comes from section 4 of the sample
plate, which holds samples 49 to 96.
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OpenArray® AccuFill™ System User Guide
Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
1
• OpenArray 3 - OpenArray plate for the third run is in Plate Holder
position 3.
– The first sample for the subarray comes from section 5 of the sample
plate, which holds samples 1 to 48.
– The second sample for the subarray comes from section 6 of the sample
plate, which holds samples 49 to 96.
• OpenArray 4 - OpenArray plate for the fourth run is in Plate Holder
position 4.
– The first sample for the subarray comes from section 7 of the sample
plate, which holds samples 1 to 48.
– The second sample for the subarray comes from section 8 of the sample
plate, which holds samples 49 to 96.
An example of two samples per subarray is shown on page 20.
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
Sample Plate
2
A
C
E
G
I
K
M
O
4
6
8
10
1
3
5
7
12
14
16
18
20
22
24
2
4
6
8
Sample 49
Sample 1
Sample 96
Sample 48
Load 1
Load 2
Sample 1
Subarray A1
Sample 49
OpenArray Plate
Sample 48
Subarray D12
Sample 96
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OpenArray® AccuFill™ System User Guide
Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
Set up the sample
plate for three
samples
1
These instructions describe how to set up a sample plate with three separate DNA
samples.
1. Label the three sections of the sample plate so that you can keep track of what is
loaded in each section. An example is shown in the following illustration.
2
A
OpenArray
1
OpenArray 1
Sample
1
Sample 1
OpenArray
11
OpenArray
Sample
3
Sample 3
6
8
10
12
14
16
1
3
5
X
C
E
G
I
OpenArray
22
OpenArray
Sample
Sample
2 2
4
K
M
O
18
20
22
24
2
4
6
X
OpenArray
1
OpenArray 1
Sample
2
Sample 2
OpenArray
OpenArray 22
Sample
Sample 11
OpenArray
OpenArray 2
Sample 3
Sample
IMPORTANT! Be sure to track where the samples are in the sample plate.
For each sample you use, Applied Biosystems recommends creating a
sample information file in CSV format. This CSV file can be used in sample
integration. See “Use Sample Integration” on page 39 for more information.
2. Use the following loading arrangement.
• OpenArray 1 - OpenArray plate for the first run is in Plate Holder position 1.
– First sample for the subarray comes from section 1 of the sample plate,
which holds samples 1 to 48.
– Second sample for the subarray comes from section 2 of the sample
plate, which holds samples 49 to 96.
– Third sample for the subarray comes from section 3 of the sample plate,
which holds samples 97 to 144.
• OpenArray 2 - OpenArray plate for the second run is in Plate Holder
position 2.
– First sample for the subarray comes from section 3 of the sample plate,
which holds samples 1 to 48.
– Second sample for the subarray comes from section 4 of the sample
plate, which holds samples 49 to 96.
– Third sample for the subarray comes from section 6 of the sample plate,
which holds samples 97 to 144.
An example of three samples per subarray is shown on page 22.
OpenArray® AccuFill™ System User Guide
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Chapter 1 Sample Preparation
Prepare sample plate for a TaqMan® OpenArray® Genotyping run
Sample 49
Sample 1
Sample 48
Sample 96
Sample Plate
2
A
C
E
G
I
K
M
O
4
6
8
10
12
14
16
18
20
22
24
2
4
6
8
1
3
5
7
Sample 97
Load 1
Load 3
Sample 144
Load 2
Sample 1
Subarray A1
Sample 49
Sample 97
OpenArray Plate
Sample 48
Sample 96
Subarray D12
Sample 144
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CHAPTER 2
Sample Loading
2
This chapter covers:
■
Materials and equipment required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
■
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
■
Important guidelines for handling the plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
■
Initialize the system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
■
Prepare the cases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
■
Prepare for loading. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
■
Load an OpenArray plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
OpenArray® AccuFill™ System User Guide
23
2
Chapter 2 Sample Loading
Materials and equipment required
Materials and equipment required
See “Ordering Information” on page 55 for a list of equipment, kits, and consumables
necessary for this procedure.
Workflow
The workflow for preparing the OpenArray® AccuFill™ instrument and OpenArray
cases summarizes the simplest loading scenario, which involves one sample and one
OpenArray.
Workflow
“Initialize the system” (page 25)
“Prepare the cases” (page 29)
“Prepare for loading” (page 29)
“Load an OpenArray plate” (page 32)
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OpenArray® AccuFill™ System User Guide
Chapter 2 Sample Loading
Important guidelines for handling the plate
2
Important guidelines for handling the plate
• Wear gloves that are one size smaller than the size you typically wear, to help
prevent excess glove material from contacting the OpenArray plate while
loading.
• Hold the OpenArray plate by the edges, at the end opposite from the barcode. Do
not touch the through-holes.
• Within one hour after opening the plate packaging, load the TaqMan OpenArray plate
with sample, place the loaded plate in a OpenArray Genotyping Case, then seal
the case.
• If you drop a loaded OpenArray plate, discard it in the appropriate waste
container.
Initialize the system
Initialize the system to prepare for the loading operation:
1. Make sure that the enclosure door is closed. Double-click the OpenArray®
AccuFill™ icon to launch the software. The software checks the computer and
connections as the system starts.
After the application has been launched, it displays a message requesting you to
clear the deck and empty the waste bin of used tips.
a. Open the instrument by grasping the enclosure door handle and gently, but
firmly, pulling the enclosure door up. The opened instrument is shown
below.
OpenArray® AccuFill™ System User Guide
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2
Chapter 2 Sample Loading
Initialize the system
Note: To safely operate the instrument, it is important to keep the
deck clear and have enough room in the waste bin to eject the used
pipette tips.
Waste bin
Plate Holder
b. Empty the waste bin and place it back on the deck.
2. If there is a Plate Holder on the deck, check if there are any OpenArray plates on
it. If necessary, remove them.
3. If there is not a Plate Holder on the deck, place one on the deck:
Orient the Plate Holder so that the text etched on it is readable, with the
barcode on the left.
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OpenArray® AccuFill™ System User Guide
Chapter 2 Sample Loading
Initialize the system
2
IMPORTANT! The locating bars and Plate Holder must be clean and
free of any foreign material. which can cause a shift in location.
To insert the Plate Holder into its place on the deck, align the top and left
edges with the metal guide bars on the deck and firmly press down. You will
hear it snap into place.
Metal guide bars
4. If necessary, replace the tip boxes.
Note: Tip boxes contain 384 tips, divided into 8 sections. When you click
Load, the AccuFill instrument loads as though a new, full box of tips is on
the deck. System software prompts you to verify that tips are in the
locations shown in the Setup Deck screen. Clicking a section in the Setup
Deck window confirms that tips are in that section of the tip box. We
recommend using a full tip box.
a. Place tip boxes into the assigned locations.
OpenArray® AccuFill™ System User Guide
27
2
Chapter 2 Sample Loading
Initialize the system
b. Place tip boxes on the deck in the two side-by-side recessed rectangular
platforms. See the illustration for the location of the tip boxes (purple and
white).
c. Remove the cover before using the tips for loading.
5. Close the door on the instrument.
6. Begin the System Self Test.
Note: System Self Test runs only at start up. The test does not run again
unless the system is restarted or a self test is intentionally run. The System
Self Test utility is in the Instrument drop-down menu in the OpenArray®
AccuFill™ application.
Click Proceed. The application performs a number of self tests and is then ready
for you to continue.
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OpenArray® AccuFill™ System User Guide
Chapter 2 Sample Loading
Prepare the cases
2
Prepare the cases
Cases for OpenArray plates are included with the OpenArray Case Sealing Station. Fill
the cases – one OpenArray plate per case – with immersion fluid:
1. Use scissors that are clean and not rusty to open a container of immersion fluid.
2. Place a case in the case rack and fill it approximately 3/4 of the way with
immersion fluid.
IMPORTANT! Immersion fluid must not be exposed to air for more than
60 minutes. Make sure that the immersion fluid is degassed. Bubbles in a
case negatively affect data quality.
Prepare for loading
To set up the software:
1. Click Setup & Load. The Setup Load Information window opens.
OpenArray® AccuFill™ System User Guide
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2
Chapter 2 Sample Loading
Prepare for loading
2. If the enclosure door on the AccuFill instrument is not open, open it by grasping
the door handle and lifting the door up.
3. Type the name of the sample plate in the Sample Plate field.
The sample plate name can also be scanned with a barcode reader, which is not
supplied with the AccuFill™ system.
4. Insert the 384-well sample plate with the foil cover still in place. Press on the plate
until you hear it snap into place.
Note: Do not remove the foil from the 384-well sample plate at this stage.
If you are using sample integration, see “Use Sample Integration” on page 39.
If you are performing multi-sample loading, see “Perform multi-sample loading”
on page 17.
5. Select 1 from the Samples Per Subarray drop-down list.
6. In the Plate Holder Position 1 text field, enter the unique serial number of the
OpenArray plate that is loaded in the first position of the Plate Holder. The
procedure to enter the serial number varies, depending on whether you use
Sample Integration:
If you are not using Sample Integration, enter the plate serial number by either:
• Typing the serial number, or
• Using a barcode reader to scan the serial number from the plate itself.
If you are using Sample Integration, enter the plate serial number using any one
of the following three methods:
• Type the serial number. There must be a file by the same name in the default
directory.
• Use a barcode reader to scan the serial number from the OpenArray plate
itself. There must be a file by the same name in the default directory.
• Click the Browse button and locate the file for the OpenArray plate.
As you enter the serial number, it is reflected in the representation of the
OpenArray plates in the lower section of the window.
Note: If you enter the name of an OpenArray plate that you have already used,
the software warns you that the name has already been used, but will not prevent
you from continuing.
7. Place the OpenArray plate into the Plate Holder. When handling OpenArray
plates:
• Always hold OpenArray plates by the edges.
• If you inadvertently drop a loaded OpenArray plate, discard it in the sharps
waste container.
• Be sure to load OpenArray plates within an hour after you open them.
Hold the OpenArray plate by the edges and place it into the Plate Holder with the
barcode face up and to the left. You can place one to four plates for one loading
run.
If you are using more than one OpenArray plate, repeat step 6 and step 7 as
necessary.
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Chapter 2 Sample Loading
Prepare for loading
2
8. By default, the AccuFill™ software identifies the next available section of the
sample plate (section 1 in the following illustration). When you choose a section
of the sample plate, you will see the corresponding color on the illustration of the
OpenArray plates at the right. You can choose only the location of the first
sample. The application automatically chooses the next available section of the
sample plate in the order shown.
For multi-sample or multi-plate loading, you can choose sections in any order by
repeating the setup procedures between plates. The setup procedure is described
in“Perform multi-sample loading” on page 17.
Note: A warning appears if you choose a sample section that you have
recently used for another loading run.
9. Click Next.
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Chapter 2 Sample Loading
Load an OpenArray plate
Load an OpenArray plate
Workflow
Load a single OpenArray plate
Remove the foil from the sample plate.
Load the OpenArray plate.
Remove the OpenArray plate.
Insert the OpenArray plate into a case.
Load multiple OpenArray plates
Remove the foil from a sample plate.
Repeat loading, removing, and encasing steps
for each OpenArray plate.
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Chapter 2 Sample Loading
Load an OpenArray plate
2
Load an OpenArray plate
To load an OpenArray plate:
1. Visually verify that the Tip Status window in the software matches the state of the
tips on the deck. Make sure that:
• Gray areas in the Tip Status window indicate that no tips are present.
• White areas indicate that tips are present.
If the software and the tips on the deck do not match, click the appropriate section
in the Tip Status window.
Note: Use tips within one week after opening the box. Discard any unused
tips after one week.
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Chapter 2 Sample Loading
Load an OpenArray plate
2. Verify each of the following conditions and, when verified, select its check box:
• Tips are configured as shown in step 1.
• Waste bin is empty.
• OpenArray plate is in the Plate Holder.
Close the Instrument Door
Note: The software will not continue until you select all the check boxes.
3. With forceps, peel off the foil covering the area of the sample plate containing the
samples to be loaded on the OpenArray plate.
4. Select the check box Remove foil from the highlighted section of the Sample
Plate.
5. Close the instrument door.
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OpenArray® AccuFill™ System User Guide
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Load an OpenArray plate
2
6. Click Load.
Note: If the number of OpenArray plates in the instrument differs from the
number that is entered in the Setup Load Information window, an error message
instructs you to remove any extra OpenArray plates. Correct the error and
continue.
You can follow the progress of the OpenArray plate loading on the screen. The
samples in each tip are loaded in the OpenArray plate. Each tip fills the
64 through-holes in one subarray, travelling in the pattern shown (the following
illustration shows the load path for only one sample):
Sections of the sample plate are loaded in a three sample/subarray order: first,
section 2, then section 1, and then section 3.
OpenArray® AccuFill™ System User Guide
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2
Chapter 2 Sample Loading
Load an OpenArray plate
7. If you are loading only one OpenArray plate, follow step a.
If you are loading more than one OpenArray plate, follow step b through step g.
a. If you are loading only one OpenArray plate, you will see the Remove
OpenArray Plate window when the load sequence is done.
Click OK.
Open the instrument,
carefully remove the
loaded OpenArray plate,
and immediately insert it
into a prepared case.
See “Insert the loaded
OpenArray® plate into a
case” on page 42. Skip
steps 7b through 7g and
proceed to “Loading
history” on page 38.
b. If you are loading more
than one OpenArray plate,
you will see the Remove
OpenArray Plate window
on page 37 when the load
sequence is done. Open
the instrument, carefully
remove the loaded
OpenArray plate and
insert it into a prepared
case immediately. See
“Insert the loaded
OpenArray® plate into a
case” on page 42.
c. Remove the foil from the
next sample plate section
as indicated by the
illustration in the window and close the enclosure door.
d. Select the Remove foil check box and click OK.
e. Close the instrument door.
f. The instrument loads the next OpenArray plate.
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OpenArray® AccuFill™ System User Guide
Chapter 2 Sample Loading
Load an OpenArray plate
2
g. Continue from step b until the last OpenArray plate has been loaded.
Note: After you have finished your experiment, clean the OpenArray
AccuFill instrument.
OpenArray® AccuFill™ System User Guide
37
2
Chapter 2 Sample Loading
Load an OpenArray plate
Loading history
The software displays the loading history, which logs the following information for the
completed load:
• OpenArray Plate Barcode
• Sample Plate Barcode
• Sample Plate Selected Area
• Sample Number
• Plate Holder Position
• Sample Load Time
• Load Status
Save the loading
history
You can save the load information by either:
• Clicking the Copy All button to capture the contents of the table. You can then
paste the data into an existing spreadsheet or word processing document. The
contents are copied in a tab-delimited format.
• Clicking the Save As button to save the contents of the table. This method saves
the data to a CSV file with a name and location of your choosing.
To not save any information, click Close.
38
OpenArray® AccuFill™ System User Guide
CHAPTER 3
Sample Integration
3
Use Sample Integration
Sample Integration combines the information about your samples – stored in a
comma-separated values (CSV) file – with the information about the pre-loaded assays
in the OpenArray®plate. The output of Sample Integration is the assignment of all
samples to their respective assays in one new updated plate file.
The following table shows the file extension used for the resulting Sample Integration
file, depending on the type of chemistry used in your analysis run.
Type of chemistry kit
SYBR® OpenArray Real-Time kits
File type
File extension
transcript
.tpf
SNP
.spf
TaqMan® OpenArray Real-Time kits
TaqMan OpenArray Genotyping Analysis kits
To use Sample Integration:
1. In the Setup Load Information window, check the Use Sample Integration check
box. A Browse button appears next to the Sample Plate field.
Use Sample Integration
Sample Plate
Browse . . .
Select Use Sample Integration to combine sample information with assay
information. This method creates a complete plate file that allows you to further
process your samples.
2. Type the name of a file in the Sample Plate field or click Browse to locate the plate
file for the sample (in CSV format). By default, sample plate files are stored in the
directory C:\OpenArray\Sample Plates.
OpenArray® AccuFill™ System User Guide
39
3
Chapter 3 Sample Integration
Use Sample Integration
3. Optionally select the Force Single Sample Loading check box to have the same
sample loaded in each subarray.
Note: When you select Force Single Sample Loading, the same sample is loaded
into each of the 64 through-holes of a subarray on the OpenArray plate, even
when the plate is formatted for two or three samples per subarray.
4. Select the OpenArray plate file provided by Applied Biosystems by typing the
name of the file in the Plate Holder Position field or click Browse to locate the
plate file for the OpenArray plate. OpenArray plate files are located in:
C:\OpenArray\OpenArray Plates
When the run is done, the integrated data is saved, with the prefix “Loaded,” by
default in:
C:\OpenArray\Loaded OpenArray Plates
5. The newly created plate file must now be used to process the OpenArray plates in
the OpenArray NT Cycler. Transfer the newly created plate file by using your
local network or some form of portable media such as a CD or a USB drive.
40
OpenArray® AccuFill™ System User Guide
CHAPTER 4
4
Prepare the plate for the NT Cycler
This chapter covers:
■
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
■
Insert the loaded OpenArray® plate into a case . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
■
Seal the OpenArray® plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
■
Frame the case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
OpenArray® AccuFill™ System User Guide
41
4
Chapter 4 Prepare the plate for the NT Cycler
Workflow
Workflow
Workflow
“Insert the loaded OpenArray® plate into a case” (page 42)
“Seal the OpenArray® plate” (page 43)
“Frame the case” (page 45)
Insert the loaded OpenArray® plate into a case
IMPORTANT! Immersion fluid in OpenArray cases must not exposed to air for
more than 60 minutes. Make sure that the immersion fluid is degassed. Bubbles
in a case negatively affect data quality.
OpenArray cases are included with the OpenArray Case Sealing Station. The front of
cases is framed in black; the back of the cases is gray. To insert the loaded OpenArray
plate into the case:
1. Gently lift the OpenArray plate from the Plate Holder with the thumb and index
finger of your left hand, placing your fingers on each side near the end with the
barcode. Keep the side with the barcode facing you. Switch hands and now hold
the OpenArray plate by the sides using your index and thumb of your right hand.
2. Hold the case at the top with the thumb and index finger of your left hand so that
the black framed side is facing you. Slide the OpenArray plate into the case so
that it sits in the rails along both inside edges of the case.
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OpenArray® AccuFill™ System User Guide
Chapter 4 Prepare the plate for the NT Cycler
Seal the OpenArray® plate
4
3. Slide the OpenArray plate all the way down into the case. The bottom of the
OpenArray should touch the bottom of the case and have approximately 1 cm
(0.39 in.) of space at the top.
4. If necessary, adjust the fluid level so it is at the top of the OpenArray plate.
Remove any excess immersion fluid with a transfer pipette.
Seal the OpenArray® plate
Seal the OpenArray plate in the case with ultraviolet (UV) glue:
Note: If your tube of glue has been open longer than two weeks, discard it and
use a new tube. Store glue in a dark place (for example, a drawer) because
ambient light can cure the glue in the tip.
1. Place a drop of UV glue on one edge of the case opening; fill until it reaches the
top of the OpenArray plate. Angle the pipette tip so that the glue reaches the
inside rail, as shown:
2. Place a similar amount of glue on the other side of the case opening, as shown:
OpenArray® AccuFill™ System User Guide
43
4
Chapter 4 Prepare the plate for the NT Cycler
Seal the OpenArray® plate
3. Add glue on each side of the case until the glue runs together in the middle. Fill
the case to the top. Make sure both the left and right sides are covered with glue,
as shown:
4. If there are air bubbles in the glue, carefully remove them by inserting a small
transfer pipette.
5. With a laboratory wipe, wipe any excess glue from the surface of the glass.
6. To cure the glue, place the OpenArray case into the Case Sealing Station:
a. Open the door. Place up to two cases into the device and close the door.
b. Turn the switch to ON. Allow the glue to cure, then turn the switch to OFF.
c. Open the door, turn the cases over so the other side faces the light. Cure the
glue again. Remove the OpenArray cases.
Instrument
44
Product
Curing time
OpenArray NT Imager
TaqMan® OpenArray Genotyping case
2 minutes
OpenArray NT Cycler
OpenArray Real-Time PCR case
3 minutes each side
OpenArray® AccuFill™ System User Guide
Chapter 4 Prepare the plate for the NT Cycler
Frame the case
4
The cases with OpenArray plates in the Case Sealing Station are shown:
Note: The Case Sealing Station emits UV light as indicated on the label (not
shown above). Keep at least 25 cm (10 in.) away from the light when operating the
Case Sealing Station.
7. If there is glue on the side of the case, carefully remove it with a razor blade.
8. Clean the case with a laboratory wipe that has been thoroughly sprayed with
ethanol. To dry the case, wipe the case downward with a clean laboratory wipe.
Gently handle the case; be sure to not apply pressure on the OpenArray plate
within the case.
Note: Dust, glue, or excess sample on the case may interfere with thermal
uniformity and can fluoresce. Make sure you thoroughly clean each case.
Frame the case
To ensure that the case achieves tight contact with the OpenArray NT Cycler thermal
block, you must adhere a frame with an adhesive pad to the OpenArray case.
Note: Framing the case does not apply to TaqMan OpenArray Genotyping Analysis
kits nor does it apply to the OpenArray NT Imager.
1. Position the OpenArray plate and case on a laboratory wipe, so that the black
framed side faces up.
2. Make sure the frame is clean, without any residual adhesive from previous runs.
3. Use scissors to cut two rectangles from the frame adhesive.
IMPORTANT! Use scissors that are clean and also not rusty.
OpenArray® AccuFill™ System User Guide
45
4
Chapter 4 Prepare the plate for the NT Cycler
Frame the case
Cut two rectangles, each about 3 mm in length, from the frame adhesive, as
shown:
4. With forceps, remove the backing from one side of the tape of one rectangle,
exposing a sticky side. Stick the tape in the middle of a long side of the frame.
5. Repeat step 4 to place adhesive on the other, long side of the assembly.
46
OpenArray® AccuFill™ System User Guide
Chapter 4 Prepare the plate for the NT Cycler
Frame the case
4
6. With forceps, peel the backing off the pieces of tape. Align two corners of the
frame with two corners of the case and bring the other corners of the frame down
onto the case. Flatten the frame against the case for 10 seconds.
The OpenArray plate is now sealed, framed, and ready to insert in the OpenArray
NT Cycler.
OpenArray® AccuFill™ System User Guide
47
4
48
Chapter 4 Prepare the plate for the NT Cycler
Frame the case
OpenArray® AccuFill™ System User Guide
CHAPTER 5
OpenArray® AccuFill™ Software
5
This chapter covers:
■
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
■
The File menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
■
The Instrument menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
■
Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
OpenArray® AccuFill™ System User Guide
49
5
Chapter 5 OpenArray® AccuFill™ Software
Overview
Overview
This chapter describes the menus available in the OpenArray® AccuFill™ software and
the commands available on them.
The File menu
Create Template Sample Plate File Folder
This command creates a sample plate file in CSV format that you can open in a
spreadsheet program such as Microsoft Excel® software. After you select the
command, type the file name in the Save As window, then click OK.
Explore OpenArray Plate File Folder
This command opens the current OpenArray plate file folder in a Windows Explorer
window. The default location of the plate file folder is C:\OpenArray\OpenArray
Plates.
Explore Sample Plate File Folder
This command opens the current sample plate file folder in a Windows Explorer
window. The default location of the plate file folder is C:\OpenArray\Sample Plates.
Explore Loaded OpenArray Plate File Folder
This command opens the current OpenArray plate file folder in a Windows Explorer
window. The default location of the plate file folder is C:\OpenArray\Loaded
OpenArray Plates.
50
OpenArray® AccuFill™ System User Guide
Chapter 5 OpenArray® AccuFill™ Software
The Instrument menu
5
The Instrument menu
Setup and Load OpenArray Plates
This command launches the Setup and Load function. Select this menu item when you
want to start a run. It is similar to the Setup and Load button.
Cancel Current Operation
This command stops the current loading operation. The menu item is active only when
you have started a run.
Show Deck
This command returns the view to the instrument deck after you have selected another
view such as the Diagnostics screen.
Show Loading History
This command opens the Loading History window. From the Loading History, you
can:
• View the record of past loading runs.
• Click the Copy All button to copy the information to an external spreadsheet
program.
• Click Save As to save the information to a CSV file.
OpenArray® AccuFill™ System User Guide
51
5
Chapter 5 OpenArray® AccuFill™ Software
The Instrument menu
Show Instrument Log
This command displays the instrument log on the right side of the screen. The log
contains a detailed list of each event that happens on the instrument. Its columns
include:
• Number – sequential numbering of the events
• Date – the date and time the event took place
• Message – a description of this event
To close the instrument log, select Hide Instrument Log from the Instrument menu.
Run System Self Test
This command displays a message telling you to clear the deck, empty the waste bin,
and close the door before moving forward with the System Self Test. After you have
completed all those tasks, clicking Proceed starts the system self test. The test runs and
displays its progress in a System Self Test window. When the test is done, the window
closes, and you can proceed with normal operation.
Edit Preferences
This command opens the Preference window that enables you to establish settings for
several software options.
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OpenArray® AccuFill™ System User Guide
Chapter 5 OpenArray® AccuFill™ Software
Help
5
The software options are:
• Require Sample Integration – When you select this option, Sample Integration is
automatically selected in the Setup Load Information window and you cannot
change that selection.
• Force Single Sample Loading – When you select Force Single Sample Loading,
Single Sample Integration is automatically selected in the Setup Load Information
window and you cannot change that selection. With Single Sample Loading, the
same sample is loaded into each of the 64 through-holes that make up a subarray
of the OpenArray plate, even when the OpenArray plate is formatted for 2 or 3
samples per subarray. This method is a convenient way to create technical
replicates for analysis.
Help
The Help menu contains information about the OpenArray AccuFill System including
a summary of the system, serial numbers, and versions of software and firmware. A
link to the Software License Agreement is also provided.
OpenArray® AccuFill™ System User Guide
53
5
54
Chapter 5 OpenArray® AccuFill™ Software
Help
OpenArray® AccuFill™ System User Guide
APPENDIX A
Ordering Information
A
This appendix covers:
■
How to order from the Applied Biosystems website . . . . . . . . . . . . . . . . . . . . . . . 56
■
Required equipment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
■
Required equipment and materials not included . . . . . . . . . . . . . . . . . . . . . . . . . . 56
■
Optional materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
■
Required reagents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
■
Required consumables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
OpenArray® AccuFill™ System User Guide
55
A
Appendix A Ordering Information
How to order from the Applied Biosystems website
How to order from the Applied Biosystems website
To order...
Instrument parts and accessories
Procedure
1. Go to www.appliedbiosystems.com.
2. Click ProductsGene
ExpressionGene Expression
Analysis Instruments OpenArray®
Real-Time PCR Platform.
Reagents
In the OpenArray Real-Time PCR Platform
page, click Related Products.
Consumables
Required equipment
The OpenArray AccuFill System (PN 4457243) includes the following components
supplied by Applied Biosystems:
Item
Part Number
OpenArray® AccuFill™ Instrument
4457244
OpenArray AccuFill Software
4457245
Computer
4398961
Monitor
4404414
Required equipment and materials not included
The following items are not supplied:
Item
56
Source
TaqMan® OpenArray Real-Time PCR
Platform
Applied Biosystems, PN 4408510
OpenArray NT Cycler System
Applied Biosystems, PN 4453106
OpenArray NT Imager
Applied Biosystems, PN 4412491
OpenArray Case Sealing Station
Applied Biosystems, PN 4409361
Uninterruptible Power Supply (UPS)
Franek PN: 5135-003 (recommended)
Electrical power strips
–
Bleach (10%)
–
DNA-ExitusPlus™
AppliChem, PN A7089
Ethanol
–
Compressed nitrogen gas
–
OpenArray® AccuFill™ System User Guide
Appendix A Ordering Information
Optional materials
A
Optional materials
Item
Source
Barcode reader
–
Fine-point silver marker
–
Required reagents
Reagents required for an OpenArray Real-Time PCR plate run:
Item
Source
Hi-Di™ Formamide
Applied Biosystems, PN 4311320
Pluronic®
Invitrogen, PN 24040-032
F-68 (10% stock)
LightCycler® FastStart DNA Master,
SYBR® Green I kit
Roche Applied Science, PN 12239264001
Albumin, bovine (BSA)
Sigma, PN A7906
SYBR®
Sigma, PN S9430
Green I
Glycerol, 99%
Sigma, PN G5150
Reagents required for a TaqMan OpenArray plate run:
Item
Source
5✕ TaqMan OpenArray® REMix Solution
Applied Biosystems, PN 4453927
GeneAmp® Fast PCR Master Mix
Applied Biosystems, PN 4362070
Albumin, bovine (BSA)
Sigma, PN A7906
OpenArray® AccuFill™ System User Guide
57
A
Appendix A Ordering Information
Required consumables
Required consumables
Item
58
Source
OpenArray 384-Well Sample Plates
Applied Biosystems, PN 4453929
OpenArray AccuFill Loader Tips
Applied Biosystems, PN 4457246
TaqMan OpenArray Genotyping Accessories Kit
Applied Biosystems, PN 4404572
– or –
– or –
OpenArray Real-Time PCR Accessories Kit
Applied Biosystems, PN 4453975
Pipettes
MLS
Forceps
MLS
Scissors
MLS
Sealing tape
MLS
OpenArray® AccuFill™ System User Guide
APPENDIX B
System Overview
B
This appendix covers:
■
OpenArray® AccuFill™ System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
■
Available run types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
OpenArray® AccuFill™ User Guide
59
B
Appendix B System Overview
OpenArray® AccuFill™ System
OpenArray® AccuFill™ System
The OpenArray® AccuFill™ System (PN 4457243) is an automated system for loading
samples from 384-well plates to OpenArray plates. The OpenArray AccuFill system
draws the master mix and sample across the surface of an OpenArray plate. The
solution does not need to be dispensed in specific volumes because the holes are selfmetering. Nor does the solution need to be forced into the holes. The same coating
process that holds liquid in the through-holes allows the liquid to be drawn in by
capillary action. Because there are no closed wells, air bubbles are not trapped during
the dispensing process.
The OpenArray® AccuFill™ instrument and its component parts are shown:
Enclosure door
Tip box
System stop button
Waste bin
Sample plate
Plate Holder
60
OpenArray® AccuFill™ User Guide
Appendix B System Overview
Available run types
B
Available run types
The loading procedure is optimized for the downstream Real-Time PCR application
on the OpenArray platform. You may choose to perform qPCR using one of the
following available chemistries: SYBR®, OpenArray Real-Time PCR, TaqMan®
OpenArray Real-Time PCR, or TaqMan OpenArray Genotyping. Use only the
chemistry that your application requires.
• For SYBR OpenArray Real-Time PCR runs (with OpenArray SYBR® Real-Time
PCR Plates), see “Prepare sample plate for a SYBR® OpenArray® real-time PCR
run” on page 10.
• For TaqMan OpenArray Real-Time PCR runs (with TaqMan OpenArray RealTime PCR Plates), see “Prepare sample plate for a TaqMan® OpenArray® realtime PCR run” on page 13.
• For TaqMan OpenArray Genotyping runs (with TaqMan OpenArray Genotyping
Plates), see “Prepare sample plate for a TaqMan® OpenArray® genotyping run”
on page 15.
OpenArray® AccuFill™ User Guide
61
B
62
Appendix B System Overview
Available run types
OpenArray® AccuFill™ User Guide
APPENDIX C
C
Cleaning the OpenArray® AccuFill™
instrument
This appendix covers:
■
Cleaning instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
■
Spill accidents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
OpenArray® AccuFill™ System User Guide
63
C
Appendix C Cleaning the OpenArray® AccuFill™ instrument
Cleaning instructions
Cleaning instructions
After you have finished your experiment, clean the OpenArray® AccuFill™instrument.
Clean the outside of the instrument
Clean the outside of the OpenArray AccuFill instrument by wiping it with a clean, dry
cloth. Do not use solvents.
Clean the inside of the instrument
Note: For chemical hazard alerts, see Appendix D, Safety.
Inside the AccuFill instrument, the waste bin and Plate Holder are removable parts
that you can clean. To clean the parts:
1. Remove the waste bin and Plate Holder from the deck of the AccuFill instrument.
2. Spray the parts with DNA-ExitusPlus™ and wait 10 minutes.
3. Rinse the parts with tap water to wash away the solution.
4. Rinse the parts with ethanol.
5. Allow the parts to dry for 5 minutes before using them again. Make sure the parts
are completely dry before loading the next plate.
Spill accidents
If liquids or other materials spill inside the AccuFill instrument, turn off the
instrument by pressing the power switch on the left side of the instrument. Unplug the
power cord from the electrical outlet. Contact Applied Biosystems service personnel.
For the latest service and support information, go to www.appliedbiosystems.com.
Power switch
Power cord outlet
64
OpenArray® AccuFill™ System User Guide
APPENDIX D
Safety
D
This appendix covers:
■
Instrumentation safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Symbols on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Locations of safety labels on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
General instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Physical hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Workstation safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . 71
■
Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
General chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Chemical waste safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Biological hazard safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
■
Safety alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
General alerts for all chemicals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Specific alerts for instrumentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
OpenArray® AccuFill™ System User Guide
65
D
Appendix D Safety
Instrumentation safety
Instrumentation safety
Symbols on instruments
Electrical
symbols on
instruments
The following table describes the electrical symbols that may be displayed on Applied
Biosystems instruments.
Symbol
Description
Indicates the On position of the main power switch.
Indicates the Off position of the main power switch.
Indicates a standby switch by which the instrument is switched on to the
Standby condition. Hazardous voltage may be present if this switch is on
standby.
Indicates the On/Off position of a push-push main power switch.
Indicates a terminal that may be connected to the signal ground reference
of another instrument. This is not a protected ground terminal.
Indicates a protective grounding terminal that must be connected to earth
ground before any other electrical connections are made to the instrument.
Indicates a terminal that can receive or supply alternating current or voltage.
Indicates a terminal that can receive or supply alternating or direct current
or voltage.
Safety symbols
The following table describes the safety symbols that may be displayed on Applied
Biosystems instruments. Each symbol may appear by itself or with text that explains
the relevant hazard (see “Safety labels on instruments” on page 8). These safety
symbols may also appear next to DANGERS, WARNINGS, and CAUTIONS that occur
in the text of this and other product-support documents.
Symbol
Description
Indicates that you should consult the manual for further information and to
proceed with appropriate caution.
Indicates the presence of an electrical shock hazard and to proceed with
appropriate caution.
Indicates the presence of a hot surface or other high-temperature hazard
and to proceed with appropriate caution.
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OpenArray® AccuFill™ System User Guide
Appendix D Safety
Instrumentation safety
Environmental
symbols on
instruments
D
The following symbol applies to all Applied Biosystems electrical and electronic
products placed on the European market after August 13, 2005.
Symbol
Description
Do not dispose of this product as unsorted municipal waste. Follow
local municipal waste ordinances for proper disposal provisions to reduce
the environmental impact of waste electrical and electronic equipment
(WEEE).
European Union customers:
Call your local Applied Biosystems Customer Service office for equipment
pick-up and recycling. See www.appliedbiosystems.com for a list of
customer service offices in the European Union.
Locations of safety labels on instruments
The caution label shown below is located on the OpenArray® AccuFill™ instrument in
two places:
• Near the power switch on the left side of the instrument
• Near the power inlet
OpenArray® AccuFill™ System User Guide
67
D
Appendix D Safety
Instrumentation safety
General instrument safety
WARNING! PHYSICAL INJURY HAZARD. Using the instrument in a manner
not specified by Applied Biosystems may result in personal injury or damage to
the instrument.
WARNING! PHYSICAL INJURY HAZARD. For safety information related to
the centrifuge and thermal cycler, refer to the manufacturer's documentation.
WARNING! PHYSICAL INJURY HAZARD. Using the centrifuge or thermal
cycler in a manner not specified by the manufacturer may result in personal
injury or damage to the instrument.
Move and lift the
instrument
CAUTION! PHYSICAL INJURY HAZARD. The instrument is to be moved and
Move and lift
stand-alone
computers and
monitors
WARNING! Do not attempt to lift or move the computer or the monitor without
positioned only by the personnel or vendor specified in the applicable site
preparation guide. If you decide to lift or move the instrument after it has been
installed, do not attempt to lift or move the instrument without the assistance of
others, the use of appropriate moving equipment, and proper lifting techniques.
Improper lifting can cause painful and permanent back injury. Depending on
the weight, moving or lifting an instrument may require two or more persons.
the assistance of others. Depending on the weight of the computer and/or the
monitor, moving them may require two or more people.
Things to consider before lifting the computer and/or the monitor:
• Make sure that you have a secure, comfortable grip on the computer or the
monitor when lifting.
• Make sure that the path from where the object is to where it is being moved is
clear of obstructions.
• Do not lift an object and twist your torso at the same time.
• Keep your spine in a good neutral position while lifting with your legs.
• Participants should coordinate lift and move intentions with each other before
lifting and carrying.
• Instead of lifting the object from the packing box, carefully tilt the box on its side
and hold it stationary while someone slides the contents out of the box.
Operate the
instrument
Ensure that anyone who operates the instrument has:
• Received instructions in both general safety practices for laboratories and specific
safety practices for the instrument.
• Read and understood all applicable Safety Data Sheets (SDSs). See “About SDSs”
on page 73.
68
OpenArray® AccuFill™ System User Guide
Appendix D Safety
Instrumentation safety
Clean or
decontaminate the
instrument
D
CAUTION! Before using a cleaning or decontamination method other than
those recommended by the manufacturer, verify with the manufacturer that the
proposed method will not damage the equipment.
Physical hazard safety
Ultraviolet light
WARNING! ULTRAVIOLET LIGHT HAZARD. Looking directly at a UV light
source can cause serious eye damage. Never look directly at a UV light source
and always prevent others from UV exposure. Follow the manufacturer’s
recommendations for appropriate protective eyewear and clothing.
Compressed gases
WARNING! PHYSICAL HAZARD. Nonflammable compressed nitrogen gas.
Contents are under pressure. Receive proper training on the handling of
compressed gases before use. Exposure to rapidly expanding gas may cause
frostbite. High concentrations of vapors in the immediate area can displace
oxygen and cause asphyxiation. Use only in areas with adequate ventilation.
Read the SDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
WARNING! EXPLOSION HAZARD. Pressurized gas cylinders are potentially
explosive and can cause severe injury if not handled properly. Always cap the
gas cylinder when it is not in use and attach it firmly to the wall or gas cylinder
cart with approved brackets or chains.
Moving parts
WARNING! PHYSICAL INJURY HAZARD. Moving parts can crush and cut.
Keep hands clear of moving parts while operating the instrument. Disconnect
power before servicing the instrument.
WARNING! PHYSICAL INJURY HAZARD. Do not operate the instrument
without the arm shield in place. Keep hands out of the deck area when the
instrument is spotting.
Solvents and
pressurized fluids
WARNING! PHYSICAL INJURY HAZARD. Always wear eye protection when
working with solvents or any pressurized fluids.
OpenArray® AccuFill™ System User Guide
69
D
Appendix D Safety
Instrumentation safety
WARNING! PHYSICAL INJURY HAZARD. To avoid hazards associated with
high-pressure fluids in polymeric tubing:
• Be aware that PEEK™ tubing is a polymeric material. Use caution when
working with any polymer tubing that is under pressure.
• Always wear eye protection when near pressurized polymer tubing.
• Extinguish all nearby flames if you use flammable solvents.
• Do not use PEEK tubing that has been severely stressed or kinked.
• Do not use PEEK tubing with tetrahydrofuran or nitric and sulfuric acids.
• Be aware that methylene chloride and dimethyl sulfoxide cause PEEK tubing
to swell and greatly reduce the rupture pressure of the tubing.
• Be aware that high solvent flow rates (~40 mL/min) may cause a static charge
to build up on the surface of the tubing. Electrical sparks may result.
Electrical safety
WARNING! ELECTRICAL SHOCK HAZARD. Severe electrical shock can
result from operating the AccuFill without its instrument panels in place. Do not
remove instrument panels. High-voltage contacts are exposed when instrument
panels are removed from the instrument.
Fuses
WARNING! FIRE HAZARD. Improper fuses or high-voltage supply can
damage the instrument wiring system and cause a fire. Before turning on the
instrument, verify that the fuses are properly installed and that the instrument
voltage matches the power supply in your laboratory.
WARNING! FIRE HAZARD. For continued protection against the risk of fire,
replace fuses only with fuses of the type and rating specified for the instrument.
Power
WARNING! ELECTRICAL HAZARD. Grounding circuit continuity is required
for the safe operation of equipment. Never operate equipment with the
grounding conductor disconnected.
WARNING! ELECTRICAL HAZARD. Use properly configured and approved
line cords for the voltage supply in your facility.
WARNING! ELECTRICAL HAZARD. Plug the system into a properly
grounded receptacle with adequate current capacity.
Overvoltage rating
70
The AccuFill system has an installation (overvoltage) category of II, and is classified as
portable equipment.
OpenArray® AccuFill™ System User Guide
Appendix D Safety
Instrumentation safety
D
Workstation safety
Correct ergonomic configuration of your workstation can reduce or prevent effects
such as fatigue, pain, and strain. Minimize or eliminate these effects by configuring
your workstation to promote neutral or relaxed working positions.
CAUTION! MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD.
These hazards are caused by potential risk factors that include but are not
limited to repetitive motion, awkward posture, forceful exertion, holding static
unhealthy positions, contact pressure, and other workstation environmental
factors.
To minimize musculoskeletal and repetitive motion risks:
• Use equipment that comfortably supports you in neutral working positions and
allows adequate accessibility to the keyboard, monitor, and mouse.
• Position the keyboard, mouse, and monitor to promote relaxed body and head
postures.
Safety and electromagnetic compatibility (EMC) standards
This section provides information on:
• U.S. and Canadian safety standards
• Canadian EMC standard
• European safety and EMC standards
• Australian EMC Standards
The OpenArray AccuFill instrument has been tested to, and complies, with the
standards listed below.
U.S. and Canadian
safety
standards
UL 61010-1:2004, 2nd Edition/CSA-C22.2 No. 61010-1, “Safety Requirements for
Electrical Equipment for Measurement, Control and Laboratory Use: Part 1: General
Requirements.”
ANSI/UL 61010-1,”Safety Requirements for Electrical Equipment for Measurement,
Control and Laboratory Use -Part 1: General Requirements.”
CAN/CSA-C22.2 #61010-1, “Safety Requirements for Electrical Equipment for
Measurement, Control and Laboratory Use -Part 1: General Requirements.”
Canadian EMC
standard
The OpenArray AccuFill instrument has been tested to, and complies with, ICES-001,
Issue 3: “Industrial, Scientific, and Medical Radio Frequency Generators.”
European safety and
EMC
standards
Safety
The OpenArray AccuFill instrument meets European requirements for safety
(2006/95/EC). This instrument has been tested to and complies with standards
EN 61010-1:2001 (second edition), “Safety Requirements for Electrical Equipment for
Measurement, Control and Laboratory Use, Part 1: General Requirements.”
OpenArray® AccuFill™ System User Guide
71
D
Appendix D Safety
Chemical safety
EMC
This instrument meets European requirements for emission and immunity
(EMC Directive 2004/108/EC). This instrument has been tested to and complies with
standard IEC 61326 (Group 1, Class A), “Electrical Equipment for Measurement,
Control and Laboratory Use – EMC Requirements.”
Australian EMC
Standards
The OpenArray AccuFill instrument has been tested to and complies with standard
AS/NZS 2064, “Limits and Methods Measurement of Electromagnetic Disturbance
Characteristics of Industrial, Scientific, and Medical (ISM) Radio-frequency
Equipment.”
Chemical safety
General chemical safety
Chemical hazard
warning
WARNING! CHEMICAL HAZARD. Before handling any chemicals, refer to
the Safety Data Sheet (SDS) provided by the manufacturer, and observe all
relevant precautions.
WARNING! CHEMICAL HAZARD. All chemicals in the instrument, including
liquid in the lines, are potentially hazardous. Always determine what chemicals
have been used in the instrument before changing reagents or instrument
components. Wear appropriate eyewear, protective clothing, and gloves when
working on the instrument.
WARNING! CHEMICAL HAZARD. Four-liter reagent and waste bottles can
crack and leak. Each 4-liter bottle should be secured in a low-density
polyethylene safety container with the cover fastened and the handles locked in
the upright position. Wear appropriate eyewear, clothing, and gloves when
handling reagent and waste bottles.
WARNING! CHEMICAL STORAGE HAZARD. Never collect or store waste in
a glass container because of the risk of breaking or shattering. Reagent and
waste bottles can crack and leak. Each waste bottle should be secured in a lowdensity polyethylene safety container with the cover fastened and the handles
locked in the upright position. Wear appropriate eyewear, clothing, and gloves
when handling reagent and waste bottles.
Chemical safety
guidelines
To minimize the hazards of chemicals:
• Read and understand the Safety Data Sheets (SDSs) provided by the chemical
manufacturer before you store, handle, or work with any chemicals or hazardous
materials. (See “About SDSs” on page 73.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the SDS.
72
OpenArray® AccuFill™ System User Guide
Appendix D Safety
Chemical safety
D
• Minimize the inhalation of chemicals. Do not leave chemical containers open. Use
only with adequate ventilation (for example, fume hood). For additional safety
guidelines, consult the SDS.
• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the
manufacturer’s cleanup procedures as recommended in the SDS.
• Comply with all local, state/provincial, or national laws and regulations related to
chemical storage, handling, and disposal.
SDSs
About SDSs
Chemical manufacturers supply current Safety Data Sheets (SDSs) with shipments of
hazardous chemicals to new customers. They also provide SDSs with the first
shipment of a hazardous chemical to a customer after an SDS has been updated. SDSs
provide the safety information you need to store, handle, transport, and dispose of the
chemicals safely.
Each time you receive a new SDS packaged with a hazardous chemical, be sure to
replace the appropriate SDS in your files.
Obtain
SDSs
The SDS for any chemical supplied by Applied Biosystems is available to you free 24
hours a day. To obtain SDSs:
1. Go to www.appliedbiosystems.com, click Support, then select SDS.
2. In the Keyword Search field, enter the chemical name, product name, SDS part
number, or other information that appears in the SDS of interest. Select the
language of your choice, then click Search.
3. Find the document of interest, right-click the document title, then select any of the
following:
• Open – To view the document
• Print Target – To print the document
• Save Target As – To download a PDF version of the document to a
destination that you choose
Note: For the SDSs of chemicals not distributed by Applied Biosystems, contact
the chemical manufacturer.
Chemical waste safety
Chemical waste
hazards
CAUTION! HAZARDOUS WASTE. Refer to Safety Data Sheets and local
regulations for handling and disposal.
WARNING! CHEMICAL WASTE HAZARD. Wastes produced by Applied
Biosystems instruments are potentially hazardous and can cause injury, illness,
or death.
OpenArray® AccuFill™ System User Guide
73
D
Appendix D Safety
Chemical safety
WARNING! CHEMICAL STORAGE HAZARD. Never collect or store waste in
a glass container because of the risk of breaking or shattering. Reagent and
waste bottles can crack and leak. Each waste bottle should be secured in a lowdensity polyethylene safety container with the cover fastened and the handles
locked in the upright position. Wear appropriate eyewear, clothing, and gloves
when handling reagent and waste bottles.
Chemical waste
safety guidelines
To minimize the hazards of chemical waste:
• Read and understand the Safety Data Sheets (SDSs) provided by the
manufacturers of the chemicals in the waste container before you store, handle, or
dispose of chemical waste.
• Provide primary and secondary waste containers. (A primary waste container
holds the immediate waste. A secondary container contains spills or leaks from
the primary container. Both containers must be compatible with the waste
material and meet federal, state, and local requirements for container storage.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the SDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open. Use
only with adequate ventilation (for example, fume hood). For additional safety
guidelines, consult the SDS.
• Handle chemical wastes in a fume hood.
• After emptying a waste container, seal it with the cap provided.
• Dispose of the contents of the waste tray and waste bottle in accordance with
good laboratory practices and local, state/provincial, or national environmental
and health regulations.
Waste disposal
If potentially hazardous waste is generated when you operate the instrument, you
must:
• Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
• Ensure the health and safety of all personnel in your laboratory.
• Ensure that the instrument waste is stored, transferred, transported, and disposed
of according to all local, state/provincial, and/or national regulations.
IMPORTANT! Radioactive or biohazardous materials may require special
handling, and disposal limitations may apply.
74
OpenArray® AccuFill™ System User Guide
Appendix D Safety
Chemical safety
D
Biological hazard safety
General biohazard
WARNING! BIOHAZARD. Biological samples such as tissues, body fluids,
infectious agents, and blood of humans and other animals have the potential to
transmit infectious diseases. Follow all applicable local, state/provincial, and/or
national regulations. Wear appropriate protective equipment, which includes
but is not limited to: protective eyewear, face shield, clothing/lab coat, and
gloves. All work should be conducted in properly equipped facilities using the
appropriate safety equipment (for example, physical containment devices).
Individuals should be trained according to applicable regulatory and company/
institution requirements before working with potentially infectious materials.
Read and follow the applicable guidelines and/or regulatory requirements in
the following:
• U.S. Department of Health and Human Services guidelines published in
Biosafety in Microbiological and Biomedical Laboratories (www.cdc.gov/od/ohs/
biosfty/bmbl5/bmbl5toc)
• Occupational Safety and Health Standards, Bloodborne Pathogens (29
CFR§1910.1030; www.access.gpo.gov/ nara/cfr/waisidx_01/
29cfr1910a_01.html).
• Your company’s/institution’s Biosafety Program protocols for working with/
handling potentially infectious materials.
Additional information about biohazard guidelines is available at:
www.cdc.gov
OpenArray® AccuFill™ System User Guide
75
D
Appendix D Safety
Safety alerts
Safety alerts
For the definitions of the alert words IMPORTANT, CAUTION, WARNING, and
DANGER, see “Safety alert words” on page 7.
General alerts for all chemicals
Avoid contact with (skin, eyes, and/or clothing). Read the Safety Data Sheets (SDSs),
and follow the handling instructions. Wear appropriate protective eyewear, clothing,
and gloves.
Specific alerts for instrumentation
WARNING! PHYSICAL INJURY HAZARD. Moving parts can crush and cut.
Keep hands clear of moving parts while operating the instrument.
WARNING! ULTRAVIOLET LIGHT HAZARD. Looking directly at a UV light
source can cause serious eye damage. Never look directly at a UV light source.
Follow the manufacturer’s recommendations for the appropriate eyewear and
clothing.
CAUTION! PHYSICAL INJURY HAZARD. Do not attempt to lift or move the
OpenArray® AccuFill™ instrument without the assistance of others, the use of
appropriate moving equipment, and proper lifting techniques. Improper lifting
can cause painful and permanent back injury. Depending on the weight,
moving or lifting an instrument may require two or more persons.
CAUTION! Do not tip the OpenArray® AccuFill instrument on end. Tipping
damages the instrument hardware and electronics and is an unsafe practice.
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OpenArray® AccuFill™ System User Guide
Documentation and Support
Related documentation
The following related documents are shipped with the system:
Document
Part
number
Description
OpenArray® AccuFill™
Site Preparation Guide
4457095
Provides information for setting up the OpenArray
AccuFill System.
OpenArray AccuFill Quick
Reference Card
4457450
Provides brief, step-by-step procedures to help you
quickly learn to use the OpenArray AccuFill
System.
The following document provides supplementary instructions:
Document
TaqMan® OpenArray
Genotyping System User
Guide
Part
number
4377476
Description
Provides information about the TaqMan OpenArray
Genotyping System, including step-by-step
procedures to:
• Prepare a TaqMan OpenArray Genotyping Plate,
using the OpenArray Autoloader and OpenArray
Case Sealing Station.
• Run a TaqMan OpenArray plate on the
OpenArray NT Imager, then analyze the data
with the OpenArray SNP Genotyping Analysis
Software.
• Maintain the TaqMan OpenArray Genotyping
Instrument Platform.
OpenArray® AccuFill™ System User Guide
77
Documentation and Support
Obtaining support
Obtaining support
To obtain additional documentation and the latest services and support information
for all locations, go to:
www.appliedbiosystems.com
At the Applied Biosystems web site, you can:
• Access worldwide telephone and fax numbers to contact Applied Biosystems
Technical Support and Sales facilities.
• Search through frequently asked questions (FAQs).
• Submit a question directly to Technical Support.
• Order Applied Biosystems user documents, SDSs, certificates of analysis, and
other related documents.
• Download PDF documents.
• Obtain information about customer training.
• Download software updates and patches.
78
OpenArray® AccuFill™ System User Guide
Glossary
case sealing station
Uses UV light to cross-link the UV-curable glue and seal the OpenArray® plates inside
cases filled with Immersion Fluid.
CSV file
Comma-separated values file that contains sample data.
frames
Black, metal, curved supports that you affix to the OpenArray cases to ensure good
contact with the thermal block on the OpenArray NT Cycler.
multi-sample
loading
Refers to the process of loading two or three samples, each from different sections of
the sample plate, into one subarray, broken into two or three distinct sections.
OpenArray
NT Real-Time PCR
instrument
Performs simultaneous thermal cycling and imaging of the OpenArray plates.
Plate Holder
Accurately positions the OpenArray plate for sample loading in the OpenArray
AccuFill System. Additional Plate Holders can be ordered from Applied Biosystems.
sample DNA
The DNA from any source of interest (e.g., tissue, whole organism, cDNA library).
sample integration
Sample Integration connects the unique identifiers for each sample to their specific
locations on an OpenArray plate. It does this using two files:
• a CSV file that describes the 384-well Sample Plate stored in the Sample Plate File
Folder
• a TPF, SPF, or EPF file that describes the OpenArray plate stored in the Open
Array Plate Input Folder
After loading the sample, the OpenArray® AccuFill™ System generates an output file
for each OpenArray plate in TPF format.
serial number
The unique alphanumeric plate identification number that is coded for each
OpenArray plate. This number is visible opposite the barcode on the plate, and is
tagged to the information contained within the plate file.
.spf file
A single nucleotide polymorphisms (SNP) plate file that is the output of Sample
Integration. It is used to process an OpenArray plate in the OpenArray NT Cycler.
SYBR
SYBR® Green I Dye, a fluorescent dye that binds preferentially to double-stranded
DNA. The optics in the OpenArray NT Cycler can detect the intensity of fluorescence
emitted from bound SYBR Green I. Based on fluorescence monitoring from SYBR
Green I, the OpenArray NT Cycler calculates the number of copies of target DNA.
OpenArray® AccuFill™ System User Guide
79
Glossary
subarray
The OpenArray plate is divided into 48 subarrays; each subarray consists of
64 through-holes in an 8x8 square configuration.
TaqMan®
A dual-labeled probe that is commonly used in laboratories for qPCR studies. The
TaqMan® OpenArray Real-Time PCR Plates qPCR platform is ideally suited for
TaqMan assays.
target DNA
The particular sequence of DNA in the sample in which your research is focused.
through-hole
Bottomless reaction wells in the OpenArray plate. There are 3072 through-holes in
each OpenArray plate. Each through-hole contains a single assay. A self-metering
loading system ensures a consistent 33-nL reaction volume within each through-hole.
Proprietary plate coatings hold reagents within the through-holes.
.tpf file
A transcript plate file that is the output of Sample Integration. It is used to process an
OpenArray plate in the OpenArray NT Cycler.
80
OpenArray® AccuFill™ System User Guide
Index
A
F
Applied Biosystems website 56
files
.spf 39
.tpf 39
comma-separated values (CSV) 18, 21, 38, 39, 79
plate 39
sample plate, OpenArray plate 50
SNP 39
storage 50
transcript 80
force single sample loading 53
B
biohazardous waste, handle 75
C
case sealing station 45, 79
cases, OpenArray® 29
CAUTION, description 7
chemical safety 72
chemical waste safety 73, 74
chemistries, available 61
cleaning instructions 15, 64
comma-separated values (CSV) file 18, 21, 38, 39, 79
compressed gases, safety. See also pressurized fluids,
safety 69
consumables, required 58
G
glossary 79
guidelines
chemical safety 72
chemical waste disposal 73
chemical waste safety 74
TaqMan® OpenArray plate, handle 25
D
H
DANGER, description 7
directories, storage 39, 40, 50
dispose waste 26
DNA samples, prepare 16
documentation 77
hazard icons. See safety symbols, on instruments
hazard symbols. See safety symbols, on instruments
hazards. See safety
Help menu 53
human DNA samples, quantify 16
E
I
edit system preferences 52
electrical safety 70
electromagnetic compatibility standards. See EMC
standards
EMC standards 71
empty waste 26
equipment and materials 56
ergonomics, safety 71
IMPORTANT, description 7
initialize the system 25
installation category 70
instrument log 52
Instrument menu 51
instrument operation, safety 68
integration, sample 39
OpenArray® AccuFill™ System User Guide
81
Index
L
load
multiple OpenArray® plates 36
multi-sample 17
OpenArray plates 29, 33
loader tips, clean 15
loading
arrangement 18, 21
force single sample 53
history 38
history, show 51
prepare for 29
three samples 21
two samples 18
log, show instrument 51
M
menus, software 50
moving and lifting safety
computers and monitors 68
instrument 68
moving parts, safety 69
multiple plates, load 36
multiple samples, load 17
N
NT Cycler plate preparation 42
O
OpenArray® AccuFill™ System
description 60
initialize 25
summary 53
turn on/off 64
OpenArray case
immersion fluid 42
seal 29
sealing station 45, 79
OpenArray plate
files 40
load multiple plates 36
loading 29
seal 42
serial number 30
setup and load 51
82
OpenArray plates
load 33
operate the instrument 68
ordering information 55
overvoltage category (rating) 70
P
physical hazard safety 69
plate files 39, 40, 50
Plate Holder 26, 79
clean 15, 64
plate loading 51
plate, sample 10, 11, 13, 15
power switch and outlet 64
preparation
case, OpenArray 29
sample 10
sample plate 11, 13, 15
pressurized fluids, safety 69
Q
quantification procedure 16
R
radioactive waste, handle 74
reagents 57
prepare 10
Real-Time PCR run 11
repetitive motion, safety 71
run types 61
Genotyping 15
Real-Time PCR 11
SYBR 10, 11
TaqMan® OpenArray Real-Time PCR 13
S
safety
before operating the instrument 68
biological hazards 75
chemical 72
chemical waste 73
compressed gases 69
electrical 70
ergonomic 71
guidelines 72, 73, 74
instrument operation 68
OpenArray® AccuFill™ System User Guide
Index
move and lift computers and monitors 68
move and lift instrument 68
moving parts 69
physical hazard 69
pressurized fluids. See also compressed gases,
safety
repetitive motion 71
solvents 69
standards 71
ultraviolet light 69
workstation 71
safety labels, on instruments 8, 67
safety standards 71
safety symbols, on instruments 66
Sample Integration 39, 53, 79
sample loading
force single 53
more than one 17
sample plate 10, 11, 13, 15
clean 15
files 39, 50
samples
load three DNA 21
load two DNA 18
preparation 10, 16
quantify human DNA 16
SDSs
about 8
description 73
obtaining 73, 78
seal plates 42
serial numbers 30, 53, 79
setup and load plates 29, 51
SNP file 39
software
license agreement 53
OpenArray® AccuFill™ software 50
options 52
versions 53
solvents, safety 69
spills, clean 64
standards
EMC 71
safety 71
storage directories 39, 40
support, technical 77
SYBR® OpenArray Real-Time PCR 10, 11, 61
symbols, safety 66
OpenArray® AccuFill™ System User Guide
System Self Test 25, 28, 51, 52
T
TaqMan® OpenArray
Genotyping 61
Genotyping run 15
Real-Time PCR 61
Real-Time PCR run 13
run 15
TaqMan OpenArray plate
guidelines for handling 25
technical support 77
training, information on 78
transcript file 39, 80
U
ultraviolet light, safety 69
W
WARNING, description 7
waste bin 26, 64
waste disposal, guidelines 74
waste profiles, description 74
workflow
load an OpenArray plate 32
plate preparation 42
sample loading 24
workstation safety 71
83
Part Number 4456986 Rev. A 06/2010
Headquarters
5791 Van Allen Way | Carlsbad, CA 92008 USA
Phone 760.603.7200
www.lifetechnologies.com
Technical Resources and Support
For the latest technical resources and support information
for all locations, please refer to our Web site at
www.appliedbiosystems.com