Thermo Fisher Scientific QuantStudio 12K Flex Real

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

QuantStudio™ 12K Flex Real–Time PCR

System

USER GUIDE

Maintenance and Administration

for use with QuantStudio™ 12K Flex Software v1.6 or later

Publication Number MAN0018832

Revision C.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256

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

Revision history:Pub.No. MAN0018832

Revision Date Description

C.0 26 July 2023

•The software version was updated to v1.6 or later.

•The list of system dyes was corrected (“System dyes” on page22, “Perform the dye calibration”

on page64 ).

•The volume for 96-well plate, 0.1mL was corrected to 30µL.

•The time for a background calibration was corrected to 5 minutes (“Background calibration” on

page51).

•The example of when to perform a dye calibration was corrected to remove the TAMRA™ dye

(“When to perform the dye calibration” on page60).

•The QuantStudio™ 12K Flex OpenArray™ Plate Press 2.0 and pipette were removed from the list of

required materials to perform a dye calibration of an OpenArray™ Plate block (“Required materials”

on page101).

•The master mix in the QuantStudio™ 12K Flex OpenArray™ Block RNase P Kit was corrected.

It is the TaqMan™ OpenArray™ Real-Time PCR Master Mix (“About the QuantStudio™ 12K Flex

OpenArray™ Block RNase P Kit” on page106).

•The instructions to load the OpenArray™ Plate for instrument veriﬁcation with OpenArray™ AccuFill™

Software v1.2 were removed.

•The list of ﬂags was corrected in the procedure to verify instrument performance with an

OpenArray™ Plate block (“Run the experiment” on page116).

•The Twister™ Robot was removed.

•The OpenArray™ Sample Tracker Software was removed.

•QuantStudio™ Design and Analysis Software v2.7 or later was added as an option to view the ROX™

dye images (“View the ROX™ dye image ﬁles” on page121).

B.0 16 February 2022

•Information about network and password security requirements was added (“Network and

password security requirements” on page19).

•Information about validating workﬂows before upgrading software was added (“Perform internal

validations before software upgrades” on page33).

•JUN™ dye and MUSTANG PURPLE™ dye were added as supported dyes.

•The speciﬁcations, electrical requirements, and environmental requirements for the QuantStudio™

12K Flex OpenArray™ AccuFill™ System were updated.

•The software installation was updated to specify that OpenArray™ Sample Tracker Software is not

applicable to OpenArray™ AccuFill™ Software v2.0 (“Software installation” on page34).

•The calibration status information was corrected in the following sections:

–“Perform the background calibration” on page54

–“Perform the uniformity calibration” on page58

–“Perform the dye calibration” on page64

•Instructions for OpenArray™ AccuFill™ Software v2.0 were added to load an OpenArray™ Plate for

RNase P instrument veriﬁcation (“Load the OpenArray™ Plate (OpenArray™ AccuFill™ Software v2.0)”

on page108).

•The instructions to seal the OpenArray™ Plate for RNase P instrument veriﬁcation were updated.

The protective ﬁlm on the outside of the lid is removed before running the plate on the

QuantStudio™ 12K Flex Instrument.

•Instructions to set up the computer were updated (“Set up the computer” on page146).

•The list of consumables was updated to correct sizes and to update the TaqMan™ Array Card

products (“Consumables” on page244).

•The list of related documents was updated (“Related documentation” on page280).

Revision Date Description

A.0 1 February 2021

Initial document release for the QuantStudio™ 12K Flex Real–Time PCR System with the QuantStudio™

12K Flex Software v1.5.

Based on QuantStudio™ 12K Flex Real–Time PCR System v1.4 Maintenance and Administration Guide

(Pub. No.4470689, Rev. C), with the following changes:

•Normalization calibration is not required for the 96-well plate blocks (0.2 mL and 0.1 mL) and the

384-well plate block.

•Updated the 96-well and 384-well spectral calibration plates.

•Added the ﬁrewall ports that must be open.

•Added ABY™ dye as a supported dye.

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

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE

LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR

ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product,

you accept the terms and conditions of all applicable Limited Use Label Licenses.

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

a trademark of Roche Molecular Systems, Inc., used under permission and license. Excel, Microsoft, Internet Explorer, and Windows

are registered trademarks of Microsoft Corporation. Cy is a registered trademark of GE Healthcare. Safari, Apple, and Macintosh are

trademarks of Apple, Inc., registered in the U.S. and other countries. Twister is a registered trademark of Caliper Life Sciences, Inc.

Mozilla and Firefox are trademarks of Mozilla Foundation in the U.S. and other countries. Adobe Reader is a trademark of Adobe, Inc.

Contents

About thisguide .......................................................... 17

Purpose ...................................................................... 17

Audience ..................................................................... 17

Assumptions .................................................................. 17

User attention words ........................................................... 17

Contents of thisguide .......................................................... 18

Network and password security requirements ..................................... 19

Network conﬁguration andsecurity .......................................... 19

Passwordsecurity ......................................................... 19

■CHAPTER1Get started .......................................................... 20

About the system .............................................................. 20

Overview of datacollection ................................................. 21

Instrument ﬁlters and supporteddyes ........................................ 22

Speciﬁcations andlayout ....................................................... 23

Systemspeciﬁcations ...................................................... 23

System layout andconnections ............................................. 28

System hardware .............................................................. 29

Instrumentcomponents .................................................... 29

Barcode reader ............................................................ 31

Electrical protectivedevices ................................................. 32

Software for the QuantStudio™ 12K Flex System ................................... 33

Perform internal validations before software upgrades .......................... 33

Computer requirements .................................................... 33

Softwareinstallation ....................................................... 34

Install third-party software .................................................. 34

Consumables for the QuantStudio™ 12K FlexInstrument ............................ 35

Compatibleconsumables ................................................... 35

Guidelines for handlingconsumables ........................................ 36

4QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

■CHAPTER2Calibrate multi-well plate and TaqMan™ Array Card

sampleblocks ..................................................................... 38

Recommended calibration and maintenanceschedule .............................. 39

Calibration with QuantStudio™ 12K Flex Software v1.6 or later ................... 40

Prepare TaqMan™ Array Cards for instrument calibration ............................ 40

Required materials ......................................................... 40

Fill the calibration TaqMan™ Array Cards ...................................... 40

ROI calibration ................................................................. 46

When to perform the calibration ............................................. 47

About the ROI calibrationdata .............................................. 47

Prepare the calibration plate or the TaqMan™ Array Card ........................ 47

Prepare the ROI calibration plate ............................................. 48

Perform the calibration ..................................................... 49

Background calibration ......................................................... 51

When to perform the calibration ............................................. 51

About the background calibrationdata ....................................... 52

Prepare the calibration plate or TaqMan™ Array Card ........................... 52

Prepare the background plate ............................................... 52

Perform the background calibration .......................................... 54

Uniformity calibration ........................................................... 56

When to perform the calibration ............................................. 56

About the uniformity calibrationdata ......................................... 56

Prepare the calibration plate or TaqMan™ Array Card ........................... 56

Prepare the calibration plate ................................................ 57

Perform the uniformity calibration ............................................ 58

Dye calibration ................................................................. 60

When to perform the dye calibration ......................................... 60

About the dye calibration ................................................... 61

Prepare the calibration plate or TaqMan™ Array Card ........................... 62

Preparing the calibration plates .............................................. 63

Perform the dye calibration ................................................. 64

Normalization calibration ........................................................ 67

When to perform the calibration ............................................. 68

About the normalization calibrationdata ...................................... 68

Preparing the calibration TaqMan™ Array Card ................................. 68

Performing the calibration ................................................... 68

Verify the instrument performance ................................................ 69

When to perform the RNase P experiment .................................... 70

About the RNase Pkits ..................................................... 70

About theanalysis ......................................................... 72

Installationspeciﬁcation .................................................... 72

Prepare the veriﬁcationconsumable ......................................... 73

Prepare the TaqMan™ RNase P Instrument Veriﬁcation Plate .................... 73

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 5

Prepare a TaqMan™ Array Card for instrumentveriﬁcation ....................... 74

Run the experiment ........................................................ 77

Troubleshooting ................................................................ 80

Identifyingcontamination ................................................... 91

■CHAPTER3Calibrate OpenArray™ Plate sampleblocks ...................... 93

Recommended calibration and maintenance ...................................... 93

About the OpenArray™ CalibrationPlaque ......................................... 94

Caring for the OpenArray™ CalibrationPlaque ................................. 95

Background calibration ......................................................... 95

Required materials ......................................................... 95

When to perform the calibration ............................................. 95

About the background calibrationdata ....................................... 96

Load the OpenArray™ CalibrationPlaque ..................................... 96

Rotate the OpenArray™ CalibrationPlaque .................................... 97

Complete the calibration .................................................... 97

Uniformity calibration ........................................................... 98

Required materials ......................................................... 98

When to perform the calibration ............................................. 98

About the uniformity calibration .............................................. 98

Load the OpenArray™ CalibrationPlaque ..................................... 99

Rotate the OpenArray™ CalibrationPlaque .................................... 99

Complete the calibration ................................................... 100

Dye calibration ............................................................... 101

Required materials ........................................................ 101

When to perform the dye calibrations ....................................... 101

About the dye calibration .................................................. 101

Guidelines for handling the OpenArray™ Calibration Cases ..................... 102

Perform the empty reading of the OpenArray™ Calibration Cases ............... 102

Perform the ﬁlled reading of the OpenArray™ Calibration Cases ................. 103

Complete the calibration ................................................... 105

Verify the instrument performance .............................................. 106

When to perform the RNase P experiment ................................... 106

About the QuantStudio™ 12K Flex OpenArray™ Block RNase PKit .............. 106

Installationspeciﬁcation ................................................... 106

Guidelines for handling the OpenArray™ Plate ................................ 107

Required materials ........................................................ 107

Prepare for the veriﬁcation experiment ...................................... 107

Load the OpenArray™ Plate (OpenArray™ AccuFill™ Software v2.0) .............. 108

Seal the OpenArray™ Plate ................................................. 112

Run the experiment ....................................................... 116

Troubleshooting .............................................................. 118

Identifyingcontamination .................................................. 121

View the ROX™ dye imageﬁles ............................................. 121

Contents

6QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

■CHAPTER4Maintenance ....................................................... 123

Regular data maintenance ..................................................... 123

Maintaining the computer harddrives ....................................... 123

Archiving and backing up experimentﬁles ................................... 123

Backing up the instrumentsettings ......................................... 124

Decontaminating the sampleblock .............................................. 124

Required materials ........................................................ 125

Handling the sampleblock ................................................. 125

Cleaning the sampleblock ................................................. 125

Replacing the instrumentfuses ................................................. 128

Required materials ........................................................ 128

Replacing thefuses ....................................................... 129

Updating the Windows™ operating system ....................................... 130

Updating the software and theﬁrmware ......................................... 130

Updating the QuantStudio™ 12K Flex Software ............................... 130

Updating the instrumentﬁrmware ........................................... 131

Managing the softwarelicenses ................................................. 131

About the software license keys andﬁles .................................... 131

Managinglicenses ........................................................ 132

Replacing the sampleblock .................................................... 133

Required materials ........................................................ 133

Handling the sampleblock ................................................. 134

Replacing the sampleblock ................................................ 134

Replacing the heatedcover .................................................... 136

Required materials ........................................................ 136

Handling the heatedcover ................................................. 137

Replacing the heatedcover ................................................ 137

Replacing the plate adapter .................................................... 139

Required materials ........................................................ 139

Replacing the plate adapter ................................................ 139

■CHAPTER5Networking ......................................................... 141

Overview ofnetworking ........................................................ 141

Control and monitor networked instruments ................................. 141

About the ethernet port .................................................... 142

Firewall ports that must beopen ............................................ 142

Example networklayouts .................................................. 143

Networking guidelines and best practices ................................... 143

Network setupworkﬂow ....................................................... 144

Collecting the required networkinformation ...................................... 144

Connecting the instrument to the network ....................................... 145

Required materials ........................................................ 145

Deﬁne the internet protocolsettings ......................................... 145

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 7

Connecting the computer to thenetwork ......................................... 145

Required materials ........................................................ 145

Computer requirement .................................................... 145

Requiredinformation ...................................................... 145

Set up the computer ...................................................... 146

Install the QuantStudio™ 12K Flex Software .................................. 146

Monitor a QuantStudio™ 12K FlexInstrument ..................................... 146

About remote monitoring .................................................. 147

Monitor the status of an instrument during a run ............................. 147

Uploading or downloading an experiment or template ......................... 148

Enable or change the calibration reminders .................................. 148

■CHAPTER6Security, audit, and electronic signature ........................ 151

Overview for administrators .................................................... 151

Exampleapplications ..................................................... 152

Conﬁgure the systemsecurity .................................................. 153

Access the Security screen and enable or disablesecurity ..................... 153

Set the account and securitypolicies ....................................... 153

Set up the messagingnotiﬁcations .......................................... 154

Manage useraccounts ........................................................ 155

Creating and editing useraccounts ......................................... 155

Determine the name of the logged-in user ................................... 156

Create or edit a user role .................................................. 156

View and print a user report ................................................ 158

Manage auditfunctions ........................................................ 159

Enable and disableauditing ................................................ 159

Select objects toaudit .................................................... 159

Create audit reasonsettings ............................................... 160

Generate audit reports ......................................................... 160

Display audit histories from the Security Settings dialog box ................... 160

Display audit histories for an experiment or template ......................... 163

Manage the electronic signature ................................................ 165

Enable or disable the electronic signature ................................... 165

Conﬁgure the meanings of the electronic signatures .......................... 165

Conﬁgure the electronic signature rights for user roles ......................... 166

Select the actions that require a signature ................................... 166

How the software prompts electronic signature ............................... 167

Generate electronic signature reports ............................................ 167

Display electronic signature records ......................................... 167

Save or print electronic signature records ................................... 167

Save or print the table of electronic signatureevents .......................... 168

Export and importsettings ..................................................... 168

Exportingsettings ........................................................ 168

Importsettings ........................................................... 168

Contents

8QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

Overview forusers ............................................................ 169

Security ..................................................................... 169

Login ................................................................... 169

Permissions .............................................................. 169

Changing your password when it expires .................................... 169

Accountsuspension ...................................................... 170

Sessiontime-out ......................................................... 170

Audit ........................................................................ 170

Electronic signature ........................................................... 170

■APPENDIXAManual instrument operation .................................... 171

Instrument touchscreenfunctions ............................................... 171

List of instrumentfunctions ................................................ 171

Operate the instrument from the touchscreen .................................... 172

Create an experiment from a template ....................................... 172

Run an experiment ........................................................ 173

Transfer experiments, templates, and results data ............................ 174

Maintain the instrument from the touchscreen .................................... 176

Backing up and restoring the instrumentsettings ............................. 176

Perform an instrument self-test ............................................. 177

Update the instrumentﬁrmware ............................................ 178

Administer the instrument from the touchscreen .................................. 179

Deﬁne the date andtime .................................................. 179

Deﬁne the instrumentsettings .............................................. 179

Deﬁne the maintenance reminders .......................................... 181

Deﬁne the networksettings ................................................ 181

Deﬁning the system shortcuts .............................................. 182

Review the instrumentstatistics ............................................ 183

Enable or disable the instrument security ................................... 183

View the instrumentlog ................................................... 184

■APPENDIXBPower on or o, store, and move the system ................. 185

Place the QuantStudio™ 12K Flex System onstandby ............................. 185

Power on the QuantStudio™ 12K Flex System .................................... 185

Power o the QuantStudio™ 12K Flex System .................................... 186

Store the QuantStudio™ 12K Flex System ........................................ 186

Required materials ........................................................ 186

Prepare the instrument for storage .......................................... 186

Move the QuantStudio™ 12K Flex System ........................................ 187

Required materials ........................................................ 187

Handle the sample block and heated cover .................................. 187

Prepare the QuantStudio™ 12K Flex Systemcomponents ...................... 187

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 9

Move the QuantStudio™ 12K Flex System ................................... 188

Reinstall the QuantStudio™ 12K Flex System ................................. 188

■APPENDIXCPrepare calibrationconsumables ............................... 190

Create a background plate or a TaqMan™ Array Card .............................. 190

Required materials ........................................................ 190

Create a background plate ................................................. 190

Create a background TaqMan™ Array Card ................................... 191

Creating a custom dye plate for calibration ....................................... 192

Before you use customdyes ............................................... 193

Required materials ........................................................ 193

Determine the optimum dye concentration ................................... 193

Create a custom dye plate ................................................. 194

Add the custom dye to the software ........................................ 195

■APPENDIXDCommand-line software operation ............................. 198

Overview of the command-line software operation ................................ 198

Command-lineworkﬂows .................................................. 198

Supporting ﬁles for experiment creation ......................................... 199

Precedence rules for experiment ﬁle generation ................................... 200

Run the command-lineapplication .............................................. 201

Run theapplication ....................................................... 201

View the command-linehelp ............................................... 201

Command syntax and arguments ............................................... 202

Batch ﬁle creation ........................................................ 202

Results export ............................................................ 204

Examples .................................................................... 205

Batch ﬁle creation ........................................................ 205

Results export ............................................................ 206

■APPENDIXEFile format reference ............................................. 207

Import formats and ﬁlespeciﬁcations ............................................ 207

About the import ﬁleformats ............................................... 207

Conventions ............................................................. 208

Plate setup ﬁleformat ......................................................... 208

File structure ............................................................. 208

Plate setup ﬁleheader ..................................................... 209

Plate setup ﬁlebody ...................................................... 209

Plate setup datacolumns .................................................. 210

Examples ................................................................ 212

Sample ﬁleformat ............................................................ 214

File structure ............................................................. 215

Exampleﬁle .............................................................. 215

Contents

10 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

Barcode ﬁleformat ............................................................ 215

File structure ............................................................. 216

Exampleﬁle .............................................................. 216

Assay informationﬁle .......................................................... 216

Export formats and ﬁlespeciﬁcations ............................................ 216

Exportformats ........................................................... 217

QuantStudio12KFlex exportformat .............................................. 217

File structure ............................................................. 218

Fileheader ............................................................... 219

Sample setupdata ........................................................ 220

Rawdata ................................................................ 222

Ampliﬁcationdata ........................................................ 223

Multicomponentdata ..................................................... 224

Resultsdata ............................................................. 224

7900 exportformat ............................................................ 232

Exportableﬁles ........................................................... 232

Setupﬁle ................................................................ 233

Fileheader ............................................................... 233

Assay (detector)data ..................................................... 233

Welldata ................................................................ 234

Multicomponentﬁle ....................................................... 234

Resultsﬁle ............................................................... 235

Standard curve, relative standard curve, and comparative Ct experiments ....... 236

Genotyping experiments ................................................... 237

RDML exportformat .......................................................... 238

More information about the RDML standard ................................. 238

■APPENDIXFParts and materials ............................................... 239

How to order ................................................................. 239

Order from the QuantStudio™ 12K Flex Software ............................. 239

Accessories .................................................................. 240

Calibration and veriﬁcationkits ................................................. 241

Calibration kits for the 384-well plateblock .................................. 242

Calibration kits for the 96-well 0.2-mL plateblock ............................ 242

Calibration kits for the 96-well 0.1-mL plateblock ............................ 243

Calibration kits for the TaqMan™ Array Cardblock ............................ 244

Consumables ................................................................ 244

■APPENDIXGGlossary ........................................................... 246

AIF .......................................................................... 246

AIX .......................................................................... 246

allele ........................................................................ 246

allelic discriminationplot ....................................................... 246

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 11

amplicon ..................................................................... 246

ampliﬁcation ................................................................. 246

ampliﬁcation eciency(EFF%) ................................................. 246

ampliﬁcationplot ............................................................. 246

ampliﬁcationstage ............................................................ 247

Analysis Settings Library ....................................................... 247

assay ........................................................................ 247

AssayID ..................................................................... 247

assay information ﬁle(AIF) ..................................................... 247

assaymix .................................................................... 247

AutoDelta .................................................................... 247

automaticbaseline ............................................................ 247

automatic threshold ........................................................... 248

background calibration ........................................................ 248

baseline ..................................................................... 248

baseline-corrected normalized reporter(ΔRn) ..................................... 248

baseline thresholdalgorithm .................................................... 248

biological replicates ........................................................... 248

blockedIPC .................................................................. 249

calibrator .................................................................... 249

chemistry .................................................................... 249

comparative Ct (ΔΔCt)method .................................................. 249

Crt .......................................................................... 249

Crtalgorithm ................................................................. 249

Ct........................................................................... 249

Ctalgorithm .................................................................. 249

customdye .................................................................. 249

Cycle threshold ............................................................... 250

cyclingstage ................................................................. 250

Cq.......................................................................... 250

datacollection ................................................................ 250

delta Rn (ΔRn)................................................................ 250

diluent ....................................................................... 250

dilution factor ................................................................ 250

dye calibration ................................................................ 250

Dye Library ................................................................... 250

EFF% ....................................................................... 250

eciency correction ........................................................... 251

endogenous control ........................................................... 251

endpoint read ................................................................ 251

Contents

12 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

error ......................................................................... 251

experiment ................................................................... 251

experimentdocument ......................................................... 251

experimentname ............................................................. 251

ExperimentSetup ............................................................ 251

experimenttype .............................................................. 252

export ....................................................................... 252

ﬁlter ......................................................................... 252

ﬂag ......................................................................... 252

forwardprimer ................................................................ 252

genotyping experiment ........................................................ 252

heterozygote ................................................................. 253

holdingstage ................................................................. 253

homozygote .................................................................. 253

housekeepinggene ........................................................... 253

import ....................................................................... 253

InstrumentConsole ........................................................... 253

InstrumentManager .......................................................... 253

internal positive control(IPC) ................................................... 253

inventoriedassays ............................................................ 254

IPC ......................................................................... 254

IPC blockingagent ............................................................ 254

IPC+ ........................................................................ 254

made-to-orderassays ......................................................... 254

manualbaseline .............................................................. 254

manual threshold ............................................................. 254

melt curve ................................................................... 254

melt curve characteristics ...................................................... 254

melt curvestage .............................................................. 254

melting temperature (Tm)....................................................... 255

melting transition region ....................................................... 255

multicomponentplot .......................................................... 255

negative control(NC) .......................................................... 255

negative control-blocked IPCwells .............................................. 255

negative control-IPCwells ..................................................... 255

no ampliﬁcation control(NAC) .................................................. 255

no template control (NTC) ...................................................... 255

nonﬂuorescent quencher-minor groove binder(NFQ-MGB) ......................... 255

normalization calibration ....................................................... 255

normalizedquantity ........................................................... 256

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 13

normalized quantitymean ...................................................... 256

normalized quantitySE ........................................................ 256

normalized reporter(Rn) ....................................................... 256

omitwell ..................................................................... 256

outlier ....................................................................... 256

passive reference ............................................................. 256

platelayout .................................................................. 256

plate setupﬁle ................................................................ 257

point ........................................................................ 257

positive control ............................................................... 257

post-PCR read ............................................................... 257

pre-PCR read ................................................................ 257

primermix ................................................................... 257

primer/probemix ............................................................. 257

puredye ..................................................................... 257

quantiﬁcation cycle (Cq)........................................................ 257

quantiﬁcationmethod ......................................................... 258

quantity ...................................................................... 258

quencher .................................................................... 258

QuickStart ................................................................... 258

R2value ..................................................................... 258

ramp ........................................................................ 258

rampspeed .................................................................. 258

raw dataplot ................................................................. 258

reactionmix .................................................................. 258

reagents ..................................................................... 258

real-timePCR ................................................................ 258

Real-time PCR Data Markup Language(RDML) ................................... 259

reference .................................................................... 259

referencesample ............................................................. 259

refSNPID .................................................................... 259

region of interest (ROI) calibration ............................................... 259

regressioncoecients ......................................................... 259

regressionline ................................................................ 259

rejectwell .................................................................... 260

relative standard curvemethod ................................................. 260

Relative Thresholdalgorithm ................................................... 260

relative threshold cycle (CRT)................................................... 260

replicate group ............................................................... 260

replicates .................................................................... 260

Contents

14 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

reporter ...................................................................... 260

reverseprimer ................................................................ 260

reverse transcriptase .......................................................... 260

Rn........................................................................... 260

ROX™dye .................................................................... 260

rsnumber .................................................................... 261

runmethod .................................................................. 261

sample ...................................................................... 261

sample deﬁnitionﬁle .......................................................... 261

Sample Library ............................................................... 261

sample/SNP assay reaction .................................................... 261

sample/target reaction ......................................................... 261

security, auditing and eSignature ............................................... 261

serial factor .................................................................. 261

slope ........................................................................ 262

SNP ......................................................................... 262

SNPassay ................................................................... 262

SNP Assay Library ............................................................ 262

stage ........................................................................ 262

standard ..................................................................... 262

standard curve ............................................................... 262

standard curvemethod ........................................................ 263

standard dilutionseries ........................................................ 263

standardquantity ............................................................. 263

startingquantity .............................................................. 263

step ......................................................................... 263

SYBR GREEN™ reagents ....................................................... 263

systemdye ................................................................... 263

TaqMan™ reagents ............................................................ 264

target ........................................................................ 264

targetcolor ................................................................... 264

Target Library ................................................................. 264

task ......................................................................... 264

technical replicates ............................................................ 264

temperatureplot .............................................................. 264

template ..................................................................... 264

templateﬁle .................................................................. 265

thermalproﬁle ................................................................ 265

threshold .................................................................... 265

threshold cycle (Ct)............................................................ 265

Contents

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 15

Tm .......................................................................... 265

touchscreen .................................................................. 265

uniformity calibration .......................................................... 265

unknown ..................................................................... 265

unknown-IPCwells ............................................................ 265

y-intercept ................................................................... 266

■APPENDIXHSafety ............................................................. 267

Symbols on thisinstrument .................................................... 267

Standard safetysymbols .................................................. 268

Additional safetysymbols ................................................. 269

Location of safetylabels ................................................... 270

Control and connectionsymbols ........................................... 271

Conformitysymbols ...................................................... 272

Safety information for instruments not manufactured by Thermo FisherScientiﬁc ..... 273

Instrumentsafety ............................................................. 273

General ................................................................. 273

Physical injury ............................................................ 273

Electricalsafety .......................................................... 274

Cleaning anddecontamination ............................................. 275

Instrument component and accessorydisposal .............................. 275

Lasersafety .................................................................. 276

Workstationsafety ............................................................ 276

Safety and electromagnetic compatibility (EMC) standards ......................... 276

Safety standards ......................................................... 277

EMC standards ........................................................... 277

Environmental design standards ............................................ 277

Chemicalsafety .............................................................. 278

Biological hazardsafety ....................................................... 279

■APPENDIXIDocumentation and support ..................................... 280

Relateddocumentation ........................................................ 280

Customer and technical support ................................................ 281

Limited product warranty ...................................................... 281

Contents

16 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

About this guide

Purpose

The QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration

Guide provides reference information for the QuantStudio™ 12K Flex Real–Time PCR System with the

QuantStudio™ 12K Flex Software v1.6 or later and describes how to prepare, maintain, and troubleshoot

the system.

For information about the QuantStudio™ 12K Flex Real–Time PCR System with the QuantStudio™ 12K

Flex Software v1.4 or earlier, see the QuantStudio™ 12K Flex Real–Time PCR System v1.4 Maintenance

and Administration Guide (Pub. No.4470689).

Audience

This user guide is written for laboratory sta who operate and maintain the QuantStudio™ 12K Flex

Real–Time PCR System.

Assumptions

This guide assumes that your QuantStudio™ 12K Flex Real–Time PCR System has been installed by a

Thermo Fisher Scientiﬁc service representative.

This guide also assumes that you have:

•Familiarity with Microsoft™ Windows™ operating system.

•Knowledge of techniques for handling and preparing DNA samples for PCR.

•A general understanding of data storage, ﬁle transfers, and copying and pasting.

User attention words

The following user attention words might appear in this document. Each word implies a particular level

of observation or action as described below:

Note: Provides information that may be of interest or help but is not critical to the use of the product.

IMPORTANT! Provides information that is necessary for proper instrument operation or accurate

chemistry kit use.

Safety alert words appear in this document with an open triangle ﬁgure that contains a hazard symbol.

These hazard symbols are identical to the hazard symbols that are axed to the instrument.

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 17

For descriptions of the safety symbols, see AppendixH, “Safety”.

Contents of this guide

You can use this guide to calibrate, service, network, and administrate the QuantStudio™ 12K Flex

Real–Time PCR System with the QuantStudio™ 12K Flex Software v1.6.

This user guide contains the following information:

•Chapter 1, “Get started”—Describes the QuantStudio™ 12K Flex Real–Time PCR System.

•Chapter 2, “Calibrate multi-well plate and TaqMan™ Array Card sample blocks”—Describes how to

maintain a QuantStudio™ 12K Flex Real–Time PCR System with a 96-well plate, a 384-well plate, or

a TaqMan™ Array Card sample block, including calibration and performance veriﬁcation.

•Chapter 3, “Calibrate OpenArray™ Plate sample blocks”—Describes how to maintain a

QuantStudio™ 12K Flex Real–Time PCR System with a TaqMan™ OpenArray™ Plate sample block,

including calibration and performance veriﬁcation.

•Chapter 4, “Maintenance”—Describes how to replace the user-serviceable parts of the

QuantStudio™ 12K Flex Real–Time PCR System and resolve infrequent problems that can occur

during normal use.

•Chapter5, “Networking”—Describes how to install the QuantStudio™ 12K Flex Real–Time PCR

System to a local area network for remote monitoring and control.

•Chapter 6, “Security, audit, and electronic signature”—Describes how to conﬁgure the security,

audit, and electronic signature functions of the software.

•Appendix A, “Manual instrument operation”—Describes how to operate the QuantStudio™ 12K Flex

Real–Time PCR System manually using the touchscreen interface.

•Appendix B, “Power on or o, store, and move the system”—Describes how to store, move, and

reinstall the components of the system.

•Appendix C, “Prepare calibration consumables”—Describes how to prepare TaqMan™ Array Cards

and TaqMan™ OpenArray™ Plates for calibration and veriﬁcation of the QuantStudio™ 12K Flex

Real–Time PCR System. The appendix also describes how to create a background plate or array

card in the event that one is unavailable, and how to create a dye plate or array card that can be

used to calibrate the system for a dye not manufactured by Thermo Fisher Scientiﬁc.

•Appendix D, “Command-line software operation”—Describes how to use the software command-

line application.

•Appendix E, “File format reference”—Provides speciﬁcations for ﬁles that the software imports,

exports, and stores.

•Appendix F, “Parts and materials”—Describes how to order parts, accessories, and consumables

for the QuantStudio™ 12K Flex Real–Time PCR System.

About this guide

Contents of this guide

18 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

Network and password security requirements

Network conﬁguration and security

The network conﬁguration and security settings of your laboratory or facility (such as ﬁrewalls, anti-

virus software, network passwords) are the sole responsibility of your facility administrator, IT, and

security personnel. This product does not provide any network or security conﬁguration ﬁles, utilities, or

instructions.

If external or network drives are connected to the software, it is the responsibility of your IT personnel

to ensure that such drives are conﬁgured and secured correctly to prevent data corruption or loss. It

is the responsibility of your facility administrator, IT, and security personnel to prevent the use of any

unsecured ports (such as USB, Ethernet) and ensure that the system security is maintained.

Password security

Thermo Fisher Scientiﬁc strongly recommends that you maintain unique passwords for all accounts in

use on this product. All passwords should be reset upon ﬁrst sign in to the product. Change passwords

according to your organization's password policy.

It is the sole responsibility of your IT personnel to develop and enforce secure use of passwords.

About this guide

Network and password security requirements

QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide 19

Get started

■ About the system ..................................................................... 20

■ Speciﬁcations andlayout .............................................................. 23

■ System hardware ..................................................................... 29

■ Software for the QuantStudio™ 12K Flex System ......................................... 33

■ Consumables for the QuantStudio™ 12K FlexInstrument .................................. 35

About the system

The Applied Biosystems™ QuantStudio™ 12K Flex Real–Time PCR System uses ﬂuorescent-based

polymerase chain reaction (PCR) reagents to provide:

•Quantitative research detection of target nucleic acid sequences (targets) using real-time analysis.

•Qualitative research detection of targets using post-PCR (endpoint) analysis.

•Qualitative analysis of the PCR product (achieved by melt curve analysis that occurs post-PCR).

1

20 QuantStudio™ 12K Flex Real–Time PCR System v1.6 or later Maintenance and Administration Guide

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Thermo Fisher Scientific QuantStudio 12K Flex Real–Time PCR System User guide

Thermo Fisher Scientific QuantStudio 12K Flex Real–Time PCR System User guide

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