Quant 3D Q150 Guide de l'utilisateur

USER GUIDEFor Research Use Only. Not for use in diagnostic procedures.QuantStudio® 3D Digital PCR Systemfor use with:QuantStudio® 3D Digital PCR Instr

The QuantStudio® 3D AnalysisSuite™ Software is a web-based application that isverified for use with the following operating systems and internet brows

d.If your selected wireless hotspot is secure, enter the required authenticationinformation (user name/password), then touch OK.If connecting your ins

c.If you elected to assign a static IP to the instrument, touch the followingfields and enter the:• IP Address – Enter the static IP address for the i

e.Touch , then configure the Windows Internet Naming Service (WINS)settings:• Windows Domain – Enter the domain name of the WINS server.• WINS Server

7.In the Network Complete screen, touch OK, then touch to return to the MainMenu.After the instrument has successfully connected to the network, the

3.In the Edit Destinations screen, touch Add to add a data destination.Note: To edit an existing destination, touch the name of the destination.4.In

• LAN data destination fields:– Target Name – Enter a name to identify the LAN data destination.Note: The target name appears within the Destination

Parts and Materials How to order from the website ... 106 General-use materials and consumables ...

Description SourceReaction tubes, DNase/RNase-free, non-stick orlow-binding: 0.5-mL or 1.5-mLFisher Scientific (Cat. no.13-864-253 or 13-864-254) or M

Cat. no.Description4485813 QuantStudio® 3D Digital PCR UV Kit• AAAA Batteries for UV-Curing Stylus (6)• UV-Activated Chip Sealant Syringe and tips• UV

Specifications and Layout Component dimensions and weights ... 109 QuantStudio® 3D Digital PCR Instrument layout and c

Getting Started About the QuantStudio® 3D Digital PCR System ... 11 Operating the instrument ...

QuantStudio® 3D Digital PCR Instrument layout and connectionsThe QuantStudio® 3D Digital PCR Instrument and the ProFlex™ 2x Flat PCR System(or Dual Fl

Electrical specificationsWARNING! For safety, the power outlet used for powering the instrumentmust be accessible at all times. In case of emergency,

Environmental requirementsEnsure that the installation room is maintained under correct environmentalconditions.Condition Acceptable RangeInstallation

Network requirementsThe QuantStudio® 3D Digital PCR Instrument supports IPv4 TCP/IP communicationand provides two methods for integrating the device i

SafetyWARNING! GENERAL SAFETY. Using this product in a manner not specifiedin the user documentation may result in personal injury or damage to thein

Symbol English FrançaisDo not dispose of this product inunsorted municipal wasteCAUTION! To minimizenegative environmentalimpact from disposal ofelec

Safety alerts on this instrumentAdditional text may be used with one of the symbols described above when morespecific information is needed to avoid e

Safety information for instruments not manufactured by ThermoFisher ScientificSome of the accessories provided as part of the instrument system are no

CAUTION! Cleaning and Decontamination. Use only the cleaning anddecontamination methods specified in the manufacturer's user documentation.It is

ReferenceDescriptionAS/NZS 2064Limits and Methods of Measurement ofElectromagnetic DisturbanceCharacteristics of Industrial, Scientific, andMedical (I

The QuantStudio® 3D Digital PCR System collects raw fluorescence data from theQuantStudio® 3D Digital PCR 20K Chip following PCR amplification.The ins

Biological hazard safetyWARNING! Potential Biohazard. Depending on the samples used on thisinstrument, the surface may be considered a biohazard. Use

Documentation and supportCustomer and technical supportVisit www.lifetechnologies.com/support for the latest in services and support,including:• World

For support visit lifetechnologies.com/support or email [email protected] February 2015

Operating the instrumentThe QuantStudio® 3D Digital PCR System can be used to perform experiments usingcompatible Applied Biosystems® reagent kits and

Prepare the QuantStudio® 3D Digital PCR System for useYou can install the QuantStudio® 3D Digital PCR System within one hour. Theinstallation requires

When planning the placement of the QuantStudio® 3D Digital PCR Systemcomponents, give special consideration to the design and organization of thelabor

Choose the instrument locationsPlacement of the QuantStudio® 3D Digital PCR Instrument and ProFlex™ 2x Flat PCRSystem (or Dual Flat Block GeneAmp® PCR

1.Plan the organization of your laboratory. Identify the locations of all stations inthe QuantStudio® 3D Digital PCR Instrument workflow, including:•

c.Remove the QuantStudio® 3D Instrument from the package and set it on aclean level surface, then remove the protective cover.d.Inspect the QuantStudi

6.If you intend to connect your instrument to a network, prepare the physicalnetwork connection:IMPORTANT! Connecting the instrument to a network is

The information in this guide is subject to change without notice.DISCLAIMERLIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANT

7.Install the QuantStudio® 3D Instrument:a.Connect the power cord to the QuantStudio® 3D Instrument, press thepower switch to the ON position, then wa

d.In the Choose Connection Type screen, select the appropriate connection:Connection ActionWired Touch LAN, then wait for the instrument to connect

e.In the Network Complete screen, touch OK.f.In the Configuration screen, touch Edit to change the instrument settings.g.In the Edit Configuration scr

h.In the Configuration screen, touch OK to accept the instrumentconfiguration.The QuantStudio® 3D Instrument is ready to use when the touchscreendispl

c.Remove the ProFlex™ PCR System Base Module from the package and set iton a clean, level surface, then remove the protective cover.5 cm (2 in)20 cm (

b.While holding the riser in place with one hand, insert the thin end of thecable tie through the opening at the base of the foot. When the end is vis

e.Using the second cable tie, repeat steps a-d to secure the riser at the otherend of the foot.dbc45°a6.Using scissors, remove the excess material fro

8.Unpack and install the sample block module:a.Open the package containing the sample block module and inspect it fordamage caused during transportati

10.Set up the ProFlex™ System:a.Open the package containing the Chip Adapters and install them.Note: Each Chip Adapter includes a set of four alignme

11.For optimal results, create a new method from the existing 3D template suppliedwith the ProFlex™ System and verify the pre-defined method for therm

ContentsAbout this guide ... 8Revision history ...

c.Remove the GeneAmp® PCR System 9700 Base Module from the packageand set it on a clean level surface, then remove the protective cover.5 cm (2 in)20

e.Inspect the Dual Flat Block Module for damage caused duringtransportation.If the instrument is damaged, note the location and appearance of thedamag

d.When the GeneAmp® PCR System 9700 displays the main menu, confirmthat the version number displayed on the screen is 3.12 or greater. If theversion n

b.Press the D/M/Y or Y/M/D soft keys until the format you want for thecurrent date displays in the Date field.c.Use the numeric keys to enter the valu

If you... Then...do not want to protect your methods press Accept (F1) again.want to protect your methods see the GeneAmp® PCR System 9700Base Module

Connect the QuantStudio® 3D AnalysisSuite™ SoftwareYou can connect to the QuantStudio® 3D AnalysisSuite™ Software before or after youinstall the Quant

Prepare Samples and LoadReactions Prepare the DNA samples ... 36 Prepare the digital PCR reactions ...

Quantitation methodsBefore performing digital PCR experiments, consider quantifying the amount ofgDNA or cDNA in each sample.We recommend the followin

If the target copy number per genome is unknown, say for a locus of unknown copiesper genome or RNA of unknown expression level, we recommend that you

In this procedure, you will prepare the PCR reactions for the samples that you intendto load to QuantStudio® 3D Digital PCR 20K Chip. The volumes of t

CHAPTER 2 Prepare Samples and Load Reactions ... 36Prepare the DNA samples ...

4.In a 0.5- or 1.5-mL low-binding reaction tube, prepare sufficient PCR reactionmix for your samples. Prepare the reaction mix at room temperature and

To ensure the proper processing and analysis of your loaded Digital PCR 20K Chip,handle them according to the following guidelines:•Always wear powder

Load the chips using the Chip LoaderThe following procedure explains how to load QuantStudio® 3D Digital PCR 20KChips automatically using a QuantStudi

Recovering from a Chip Loader errorPerform the following steps if the QuantStudio® 3D Digital PCR Chip Loader statuslight flashes red, indicating that

IMPORTANT! Confirm that the tip is locked firmly in place before proceeding.Keep out of sunlight32141Plunger2UV-Activated Chip Sealant Syringe3Chip

4.Load the PCR reaction onto a Digital PCR 20K Chip:a.Open the QuantStudio® 3D Digital PCR 20K Chip package, then gentlygrasp the chip by its sides an

c.Remove the red protective film from a QuantStudio® 3D Digital PCR ChipCase Lid, press the Lid Nest button ( ), carefully place the Chip Case Lidinto

e.Press the black loading button on the Chip Loader to load the Digital PCR20K Chip.IMPORTANT! Before pressing the loading button, confirm that the S

5.Rotate the Chip Loader arm so that the Chip Case Lid solidly contacts the DigitalPCR 20K Chip, firmly press down for 15 seconds to ensure a tight se

7.Seal the Chip Case using Chip Sealant:a.Hold the syringe tip just above (or in slight contact with the inside wall) ofthe fill port of the sealed Ch

CHAPTER 4 Analyze the Prepared Chips ... 66Using the QuantStudio® 3D Digital PCR Instrument ...

c.When the light powers off (approximately ³15 seconds), remove the chipand place it on a clean, dry, lint-free surface.IMPORTANT! Remove the Digital

• Immersion Fluid Tip•UV-Activated Chip Sealant Syringe• UV-Curing Stylus for Chip Sealant• UV-Curing Stylus Stand• Isopropanol• Gloves, powder-free,

IMPORTANT! Confirm that the tip is locked firmly in place before proceeding.Keep out of sunlight32141Plunger2UV-Activated Chip Sealant Syringe3Chip

4.Remove the following consumables from their packaging and place them on aclean, dry, lint-free surface:• QuantStudio® 3D Digital PCR Chip Case Lid•

c.While holding the Sample Loading Blade at a 70-80° angle relative to theheated block so that the port faces up, place the edge of the blade at the e

7.Seal the Digital PCR 20K Chip:a.Remove the red protective film from the QuantStudio® 3D Digital PCR ChipCase Lid, then carefully place it onto the p

9.Seal the Chip Case using Chip Sealant:a.Hold the syringe tip just above (or in slight contact with the inside wall) ofthe fill port of the sealed Ch

10.Visually inspect the sealed Digital PCR 20K Chip for potential problems:• Leaks – Confirm that no Immersion Fluid is leaking from the fill port ora

Perform the PCR Choosing a thermal cycler ... 58 Thermal cycle the Digital PCR 20K Chips ...

Before running each batch of Digital PCR 20K Chips, perform the following to ensureefficient thermal cycling:•Confirm that the following parts are ins

APPENDIX B Networking ... 95Networking overview ...

• Confirm the thermal cycler is running the correct firmware version number tothermal cycle Digital PCR 20K Chips:– ProFlex™ 2x Flat PCR System – The

Table 5 GeneAmp® PCR System 9700 PCR MethodPCR ProtocolRunSpeedReactionVolumeStage 1 Stage 2 Stage 396.0°C 60.0°C 98.0°C 60.0°C 10.0°C[1]Standard 2

To ensure the proper function of your loaded Digital PCR 20K Chips, handle the ChipCases according to the following guidelines:•Always wear powder-fre

3.Load the QuantStudio® 3D Digital PCR 20K Chips into the thermal cycler:a.Place the sealed Digital PCR 20K Chips onto the sample block so that the fi

4.Use the thermal cycler to select and start the pre-programmed run for the DigitalPCR 20K Chips. See the ProFlex™ PCR System User Guide (Pub. no. MAN

3.Remove the Chip Adapters from the thermal cycler sample block and place themon a clean, dry surface. Remove the Digital PCR 20K Chips from the ChipA

Analyze the Prepared Chips Using the QuantStudio® 3D Digital PCR Instrument ... 66 Analyze the chips ...

The following figure shows the workflow for running a single QuantStudio® 3DDigital PCR 20K Chip on the QuantStudio® 3D Digital PCR Instrument.StartqL

The QuantStudio® 3D Digital PCR Instrument features a simple interface for readingthermal cycled QuantStudio® 3D Digital PCR 20K Chips.65431 21Network

Analyze the chipsThe following materials are required to image loaded Digital PCR 20K Chips on theQuantStudio® 3D Digital PCR System.• Prepared Digita

Documentation and support ... 121Customer and technical support ...

2.(Optional) Enter a prefix to apply to each experiment (.eds) file name:a.From the Main Menu of the QuantStudio® 3D Instrument, touch , thentouch In

The touchscreen displays the USB drive icon ( ) when the QuantStudio® 3DInstrument has mounted the USB drive.2.Open the chip tray and load the Digital

3.In the instrument touchscreen, wait for the QuantStudio® 3D Instrument todetect and image the chip.IMPORTANT! Do not open the chip tray or remove t

5.After reviewing the results of the run, open the chip tray and remove the chip (orremove the USB drive, if present) to close the results screen.If t

The QuantStudio® 3D Digital PCR Instrument displays a summary of the imagingdata after each successful run. For each QuantStudio® 3D Digital PCR 20K C

Data quality flags generated and displayed by the software are a measure of theoverall chip quality, based on well quality thresholds and other data a

If a data transfer is unsuccessful, you can use the QuantStudio® 3D Instrument RunHistory screen to transfer experiment files to a USB drive for manua

The Run History screen displays the data transfer status next to each file in theinstrument memory:• Pass – The instrument successfully transferred th

When deployed in cloud configuration, the AnalysisSuite™ Software is accessed as aweb-based application that can be run using any compatible web brows

TroubleshootingTroubleshooting chip images using the Chip ViewThe following table summarizes some of the more common problems that can affectimaging o

About this guideCAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazardtypes specified in procedures may be abbreviated in this document. For t

Observation Possible Cause ActionA bubble was present in theSample Loading Blade when itwas used to apply the PCRreaction to the Digital PCR 20KChip.I

Observation Possible Cause Action• The Digital PCR 20K Chipleaked during thermalcycling or imaging.• A large bubble was presentin the chip (insufficie

Observation Possible Cause ActionChip was not completely coveredwith Immersion Fluidimmediately after loading (whilestill on the chip loader or heated

Observation Possible Cause ActionCondensation may have beenpresent on the Digital PCR 20KChip during imaging.IMPORTANT! Condensationmay not be visibl

Observation Possible Cause ActionExcess template was loaded ontothe chip.In the QuantStudio® 3DAnalysisSuite™ Software, checkthe copies per reaction a

Observation Possible Cause ActionToo much sample was left inloading blade.Ensure that you are loading only14.5 µL of reaction mix into theloading blad

Maintenance Cleaning the chip tray and sample block ... 86 Configure the instrument settings ...

CAUTION! PHYSICAL INJURY HAZARD. Do not remove the covers to theQuantStudio® 3D Instrument or thermal cycler. There are no components insidethe instr

Configure the instrument settingsAfter you install the QuantStudio® 3D Digital PCR Instrument, you can configure theinstrument settings for your regio

Use this procedure to manually configure the time zone, date, and time settings foryour instrument.Note: If connected to a network, the QuantStudio®

PrerequisitesThis guide also assumes that you have:• Knowledge of techniques for handling and preparing samples for PCR.• A general understanding of d

To return your instrument for service:1.Contact your local customer care center or technical support group (see “Customer and technical support“ on pa

CAUTION! FIRE HAZARD. For continued protection against the risk of fire,replace fuses only with listed and certified fuses of the same type and ratin

1.Download the firmware update:a.Go to www.lifetechnologies.com/supportb.Go to Instrument Management (you will need to log in if not alreadylogged in

Calibrate the touchscreenCalibrate the instrument touchscreen periodically as part of the routine maintenanceof your instrument, if you observe a decr

4.(Optional) Export the system log to a USB drive:a.Plug the drive into the USB port on the front of the QuantStudio® 3DInstrument.b.In the Instrument

Networking Networking overview ... 95 Connect the instrument to the network ...

The wireless dongle sold for use with the QuantStudio® 3D Digital PCR Instrumentcan be installed to an internal USB port behind the rear panel to enab

ConnectionMaterialsWired CAT6 Ethernet cable of sufficient length with RJ45 connectors (for a1000Mbit/s network connection or a CAT5 for a 100Mbit/s c

1.Prepare the physical connection to the network:Connection ActionWired1. Power on the QuantStudio® 3D Instrument.2. Connect one end of a standard cat

3.Choose the appropriate option:If connecting your instrument to a… ActionWired network that supports DHCP Network setup is complete.Note: The QuantS