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ECL`

ExperimentqPCR

ExperimentqPCR[Samples,PrimerPairs]⟹Protocol

creates a Protocol object for running a quantitative Polymerase Chain Reaction (qPCR) experiment, which uses a thermocycler to amplify and quantify target sequences from the Samples using PrimerPairs and either a fluorescent intercalating dye or fluorescently labeled probes.

ExperimentqPCR[Samples,ArrayCard]⟹Protocol

creates a Protocol object for running a quantitative polymerase chain reaction (qPCR) experiment, which uses a thermocycler to amplify and quantify target sequences from the Samples using an ArrayCard containing primer pairs and fluorescently labeled probes.

    
ExperimentqPCR allows real-time monitoring of the amplification of target sequences from nucleic acid templates during Polymerase Chain Reaction (PCR). The reaction products are detected via either duplex staining dyes or sequence-specific reporter-labeled probes, and the resulting data can be used for quantitative/semi-quantitative analysis of the sequences of interest.
    

Experimental Principles

    Figure 1.1: Step 1: Reaction mixtures are prepared in a 384-well qPCR plate. Step 2: The polymerase can be heat-activated in hot start PCR. Steps 3-6: The samples undergo the thermocycling procedure, which includes denaturation, annealing, and extension, and the amplification products are detected via dyes or probes following each cycle. Step 7: The qPCR data are analyzed via AnalyzeQuantificationCycle and AnalyzeCopyNumber.

Instrumentation

    ViiA 7

    Figure 2.1.1: The ViiA 7 offers real-time monitoring of target sequence amplification during 384-well plate-based PCR procedures. The thermocycling profile is programmable in the temperature range from 4 °C to 100 °C, with a maximum ramp rate of 3.4 °C/sec. The ViiA 7's excitation wavelengths of 470, 520, 550, 580, 640, and 662 nm and emission wavelengths of 520, 558, 586, 623, 682, and 711 nm allow monitoring of the amplification targets via a variety of dyes or reporters.

Experiment Options

    General

    Instrument

    The instrument for running the quantitative polymerase chain reaction (qPCR) experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, Thermocycler] or Object[Instrument, Thermocycler]
    Programmatic Pattern: ObjectP[{Model[Instrument, Thermocycler], Object[Instrument, Thermocycler]}] | Automatic

    ReactionVolume

    The total volume of the reaction including the sample, primers, probes, dyes and master mix. If using an array card, the final reaction volume in the microfluidic well following centrifugation.
    Default Value: Automatic
    Default Calculation: Automatically set to 2 Microliter if using an array card, or 20 Microliter otherwise.
    Pattern Description: Greater than or equal to 2 microliters and less than or equal to 50 microliters.
    Programmatic Pattern: RangeP[2*Microliter, 50*Microliter] | Automatic

    MasterMix

    The stock solution composed of enzymes (DNA polymerase and optionally reverse transcriptase), buffer, dyes and nucleotides used to amplify cDNA or gDNA.
    Default Value: Automatic
    Default Calculation: Automatically set based on DuplexStainingDye and ReverseTranscription.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic

    MasterMixVolume

    The volume of the master mix to add to the reaction. If using an array card, the initial volume of the master mix to be mixed with the sample then loaded into the array card reservoir.
    Default Value: Automatic
    Default Calculation: Automatically set based on ReactionVolume and MasterMix.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters.
    Programmatic Pattern: RangeP[0.5*Microliter, 50*Microliter] | Automatic

    StandardVolume

    The volume of the standard to add to the reaction.
    Default Value: Automatic
    Default Calculation: Resolved automatically to 2 Microliter if a Standard is included in the experiment.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null

    Buffer

    The chemical or stock solution used to bring each reaction to ReactionVolume once all other components have been added.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,"Milli-Q water"] if after the addition of all reaction components the volume has not reached ReactionVolume, or Null otherwise.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic

    SampleVolume

    The volume of the sample from which the target will be amplified to add to the reaction. If using an array card, the initial volume of the sample to be mixed with the master mix then loaded into the array card reservoir.
    Default Value: Automatic
    Default Calculation: Automatically set to 48 Microliter if using an array card, or 2 Microliter otherwise.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters.
    Programmatic Pattern: RangeP[0.5*Microliter, 50*Microliter] | Automatic
    Index Matches to: experiment samples

    BufferVolume

    The volume, if any, of buffer added to bring the total volume up to ReactionVolume (if using an array card, ReactionVolume*48).
    Default Value: Automatic
    Default Calculation: Automatically set to a value based on the volume of all other reaction components.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters.
    Programmatic Pattern: RangeP[0.5*Microliter, 50*Microliter] | Automatic
    Index Matches to: experiment samples

    ForwardPrimerVolume

    The total volume of each forward primer to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if ArrayCard is True, otherwise it is set to ReversePrimerVolume (if specified) or 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or list of one or more greater than or equal to 0.5 microliters and less than or equal to 50 microliters entries.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | {RangeP[0.5*Microliter, 50*Microliter]..}) | Automatic
    Index Matches to: experiment samples

    ReversePrimerVolume

    The total volume of each reverse primer to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if ArrayCard is True, otherwise it is set to ForwardPrimerVolume (if specified) or 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or list of one or more greater than or equal to 0.5 microliters and less than or equal to 50 microliters entries.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | {RangeP[0.5*Microliter, 50*Microliter]..}) | Automatic
    Index Matches to: experiment samples

    Probe

    The short oligomer strand containing a reporter and quencher, which when separated during the synthesis reaction will result in fluorescence.
    Default Value: Automatic
    Default Calculation: Automatically set to the sample from the array card if ArrayCard is True, or Null otherwise.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or list of one or more an object of type or subtype Model[Sample] or Object[Sample] or a prepared sample entries or Null.
    Programmatic Pattern: (((ObjectP[{Model[Sample], Object[Sample]}] | _String) | {(ObjectP[{Model[Sample], Object[Sample]}] | _String)..}) | Automatic) | Null
    Index Matches to: experiment samples

    ProbeVolume

    The volume of the probe to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if ArrayCard is True or Probe is Null, or 1 Microliter otherwise.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or list of one or more greater than or equal to 0.5 microliters and less than or equal to 50 microliters entries or Null.
    Programmatic Pattern: ((RangeP[0.5*Microliter, 50*Microliter] | {RangeP[0.5*Microliter, 50*Microliter]..}) | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousPrimerPair

    The pair of short oligomer strands designed to amplify an endogenous control gene (such as a housekeeping gene) whose expression should not different between samples.
    Default Value: Null
    Pattern Description: {Forward Primer, Reverse Primer} or Null.
    Programmatic Pattern: {ObjectP[{Model[Sample], Object[Sample]}] | _String, ObjectP[{Model[Sample], Object[Sample]}] | _String} | Null
    Index Matches to: experiment samples

    EndogenousForwardPrimerVolume

    The total volume of each endogenous control forward primer to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically resolves to match EndogenousReversePrimerVolume; otherwise, defaults to 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousReversePrimerVolume

    The total volume of each endogenous control reverse primer to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically resolves to match EndogenousForwardPrimerVolume; otherwise, defaults to 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousProbe

    The short oligomer strand containing a reporter and quencher, which when separated during the synthesis reaction will result in fluorescence.
    Default Value: Null
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Model[Sample], Object[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    EndogenousProbeVolume

    The volume of the probe to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 Microliter if an endogenous probe is being used.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: experiment samples

    NumberOfReplicates

    Number of times each of the input samples should be analyzed using identical experimental parameters.
    Default Value: Null
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: GreaterEqualP[2, 1] | Null

    Post Experiment

    AssayPlateStorageCondition

    The conditions under which the thermocycled 384-well assay plate from this experiment should be stored after the protocol is completed. The assay plate is discarded by default.
    Default Value: Automatic
    Default Calculation: Automatically set to Disposal if using a 384-well plate, or Null otherwise.
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null

    ArrayCardStorageCondition

    The conditions under which the thermocycled array card from this experiment should be stored after the protocol is completed. The array card is discarded by default.
    Default Value: Automatic
    Default Calculation: Automatically set to Disposal if using an array card, or Null otherwise.
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null

    MasterMixStorageCondition

    The non-default condition under which the master mix used in this experiment should be stored after the protocol is completed. If left unset, the master mix will be stored according to its current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    StandardStorageCondition

    The non-default conditions under which the standards of this experiment should be stored after the protocol is completed. If left unset, the standards will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: Standard

    StandardForwardPrimerStorageCondition

    The non-default conditions under which the forward primers for the standards of this experiment should be stored after the protocol is completed. If left unset, the forward primers for standards will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: Standard

    StandardReversePrimerStorageCondition

    The non-default conditions under which the reverse primers for the standards of this experiment should be stored after the protocol is completed. If left unset, the reverse primers for standards will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: Standard

    StandardProbeStorageCondition

    The non-default conditions under which the probes for the standards of this experiment should be stored after the protocol is completed. If left unset, the probes for standards will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: Standard

    ForwardPrimerStorageCondition

    The non-default conditions under which the forward primers of this experiment should be stored after the protocol is completed. If left unset, the forward primers will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or list of one or more {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal entries or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | {(SampleStorageTypeP | Disposal)..}) | Null
    Index Matches to: experiment samples

    ReversePrimerStorageCondition

    The non-default conditions under which the reverse primers of this experiment should be stored after the protocol is completed. If left unset, the reverse primers will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or list of one or more {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal entries or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | {(SampleStorageTypeP | Disposal)..}) | Null
    Index Matches to: experiment samples

    ProbeStorageCondition

    The non-default conditions under which the probes of this experiment should be stored after the protocol is completed. If left unset, the probes will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or list of one or more {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal entries or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | {(SampleStorageTypeP | Disposal)..}) | Null
    Index Matches to: experiment samples

    EndogenousForwardPrimerStorageCondition

    The non-default conditions under which the endogenous forward primers of this experiment should be stored after the protocol is completed. If left unset, the endogenous forward primer will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: experiment samples

    EndogenousReversePrimerStorageCondition

    The non-default conditions under which the endogenous reverse primers of this experiment should be stored after the protocol is completed. If left unset, the endogenous reverse primer will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: experiment samples

    EndogenousProbeStorageCondition

    The non-default conditions under which the endogenous probes of this experiment should be stored after the protocol is completed. If left unset, the endogenous probe will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null
    Index Matches to: experiment samples

    SamplesInStorageCondition

    The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

    Reverse Transcription

    ReverseTranscription

    Indicates if one-step reverse transcription is performed in order to convert RNA input samples to cDNA.
    Default Value: Automatic
    Default Calculation: Automatically set to True if any reverse transcription related options are set, and False if none are set.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    ReverseTranscriptionTime

    The length of time for which the reaction volume will held at ReverseTranscriptionTemperature in order to convert RNA to cDNA.
    Default Value: Automatic
    Default Calculation: Automatically set to 15 minutes if ReverseTranscription is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 2 hours or Null.
    Programmatic Pattern: (RangeP[0*Second, 2*Hour] | Automatic) | Null

    ReverseTranscriptionTemperature

    The initial temperature at which the sample should be heated to in order to activate the reverse transcription enzymes in the master mix to convert RNA to cDNA.
    Default Value: Automatic
    Default Calculation: Automatically set to 48 degrees Celsius if ReverseTranscription is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 100*Celsius] | Automatic) | Null

    ReverseTranscriptionRampRate

    The rate at which the reaction volume is heated to bring the sample to the reverse transcription temperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 1.6 Celsius/Second if ReverseTranscription is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)] | Automatic) | Null

    Polymerase Activation

    Activation

    Indicates if polymerase hot start activation is performed. In order to reduce non-specific amplification, modern enzymes can be made room temperature stable by inhibiting their activity via thermolabile conjugates. Once an experiment is ready to be ran, this inhibition is removed by heating the reaction to ActivationTemperature.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    ActivationTime

    The length of time for which the reaction volume is held at ActivationTemperature in order to a remove the thermolabile conjugates inhibiting enzyme activity.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 minute if Activation is set to True.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 2 hours or Null.
    Programmatic Pattern: (RangeP[0*Second, 2*Hour] | Automatic) | Null

    ActivationTemperature

    The temperature at which at which the thermolabile conjugates inhibiting enzyme activity are removed.
    Default Value: Automatic
    Default Calculation: Automatically set to 95 degrees Celsius if Activation is set to True.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 100*Celsius] | Automatic) | Null

    ActivationRampRate

    The rate at which the reaction is heated to bring the sample to the ActivationTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 1.6 degrees Celsius per second if Activation is set to True.
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)] | Automatic) | Null

    Denaturation

    DenaturationTime

    The length of time for which the reaction is held at DenaturationTemperature in order to separate any double stranded template DNA into single strands.
    Default Value: 30 seconds
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 2 hours.
    Programmatic Pattern: RangeP[0*Second, 2*Hour]

    DenaturationTemperature

    The temperature to which the sample is heated in order to disassociate double stranded template DNA into single strands.
    Default Value: 95 degrees Celsius
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius.
    Programmatic Pattern: RangeP[4*Celsius, 100*Celsius]

    DenaturationRampRate

    The rate at which the reaction is heated to bring the sample to DenaturationTemperature.
    Default Value: 1.6 degrees Celsius per second
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second.
    Programmatic Pattern: RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)]

    Primer Annealing

    PrimerAnnealing

    Indicates if annealing should be performed as a separate step instead of as part of extension. Lowering the temperature during annealing allows primers to bind to template DNA to serve as anchor points for DNA polymerization in the subsequent extension stage.
    Default Value: Automatic
    Default Calculation: Automatically set to True if any primer annealing related options are set, and False if none are set.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    PrimerAnnealingTime

    The length of time for which the reaction is held at PrimerAnnealingTemperature in order to allow binding of primers to the template DNA.
    Default Value: Automatic
    Default Calculation: Automatically set to 30 second if PrimerAnnealing is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 2 hours or Null.
    Programmatic Pattern: (RangeP[0*Second, 2*Hour] | Automatic) | Null

    PrimerAnnealingTemperature

    The temperature to which the sample is heated in order to allow primers to bind to the template strands.
    Default Value: Automatic
    Default Calculation: Automatically set to 60 Celsius if PrimerAnnealing is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 100*Celsius] | Automatic) | Null

    PrimerAnnealingRampRate

    The rate at which the reaction is heated to bring the sample to PrimerAnnealingTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 1.6 Celsius/Second if PrimerAnnealing is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)] | Automatic) | Null

    Strand Extension

    ExtensionTime

    The length of time for which the polymerase synthesizes a new DNA strand using the provided primer pairs and template DNA.
    Default Value: 60 seconds
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 2 hours.
    Programmatic Pattern: RangeP[0*Second, 2*Hour]

    ExtensionTemperature

    The temperature at which the sample is held to allow the polymerase to synthesis new DNA strand from the template DNA.
    Default Value: 72 degrees Celsius
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius.
    Programmatic Pattern: RangeP[4*Celsius, 100*Celsius]

    ExtensionRampRate

    The rate at which the reaction is heated to bring the sample to ExtensionTemperature.
    Default Value: 1.6 degrees Celsius per second
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second.
    Programmatic Pattern: RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)]

    NumberOfCycles

    The number of times the samples will undergo repeated cycles of melting, annealing and extension.
    Default Value: 40
    Pattern Description: Greater than or equal to 1 and less than or equal to 60.
    Programmatic Pattern: RangeP[1, 60]

    Melting Curve

    MeltingCurve

    Indicates if melt curve should be performed at the end of the experiment. The fluorescence of the DuplexStainingDye is monitored while the sample is slowly heated, allowing detection of products with different melting temperatures.
    Default Value: Automatic
    Default Calculation: Automatically set to True for dye based assays and False to probe based assays.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    MeltingCurveStartTemperature

    The temperature at which to start the melting curve.
    Default Value: Automatic
    Default Calculation: Automatically set to 60 Celsius if MeltingCurve is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 100*Celsius] | Automatic) | Null

    MeltingCurveEndTemperature

    The temperature at which to end the melting curve.
    Default Value: Automatic
    Default Calculation: Automatically set to 95 Celsius if MeltingCurve is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 100*Celsius] | Automatic) | Null

    PreMeltingCurveRampRate

    The rate at which the temperature is decreased in order to bring the samples to MeltingCurveStartTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 1.6 Celsius/Second if MeltingCurve is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0.002 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.002*(Celsius/Second), 3.4*(Celsius/Second)] | Automatic) | Null

    MeltingCurveRampRate

    The rate at which the temperature is increased during in order to bring the samples from MeltingCurveStartTemperature to MeltingCurveEndTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to .015 Celsius/Second if MeltingCurve is set to True, and Null if it is set to False.
    Pattern Description: Greater than or equal to 0.015 degrees Celsius per second and less than or equal to 3.4 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.015*(Celsius/Second), 3.4*(Celsius/Second)] | Automatic) | Null

    MeltingCurveTime

    The length of time it takes to change the temperature of the sample from MeltingCurveStartTemperature to MeltingCurveEndTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to a value based on MeltingCurveRampRate.
    Pattern Description: Greater than or equal to 0.01 seconds and less than or equal to 24 hours or Null.
    Programmatic Pattern: (RangeP[0.01*Second, 24*Hour] | Automatic) | Null

    Dye Staining

    DuplexStainingDye

    The fluorescent dye present in the reaction which intercalates between the base pairs of a double stranded DNA.
    Default Value: Automatic
    Default Calculation: Automatically set to the duplex stain dye part of the MasterMix for dye based assay or Null if one isn't present.
    Pattern Description: An object of type or subtype Object[Sample], Model[Sample], or Model[Molecule] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample], Model[Molecule]}] | _String) | Automatic) | Null

    DuplexStainingDyeVolume

    The volume of the fluorescent dye to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if the dye is already part of the master mix or 1 Microliter if it is being added separately.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 200 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 200*Microliter] | Automatic) | Null

    ReferenceDye

    The fluorescent dye present in the reaction which does not takes part of the reaction and is used for signal normalization.
    Default Value: Automatic
    Default Calculation: Automatically set to the passive dye present in the master mix.
    Pattern Description: An object of type or subtype Object[Sample], Model[Sample], or Model[Molecule] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample], Model[Molecule]}] | _String) | Automatic) | Null

    ReferenceDyeVolume

    The volume of the fluorescent reference dye to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to Null when using a pre-made master mix.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null

    Detection

    DuplexStainingDyeExcitationWavelength

    The wavelength of light used to excite the fluorescent reporter dye.
    Default Value: Automatic
    Default Calculation: Automatically set to the wavelength excitation wavelength of the DuplexStainingDye
    Pattern Description: 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers or Null.
    Programmatic Pattern: (qPCRExcitationWavelengthP | Automatic) | Null

    DuplexStainingDyeEmissionWavelength

    The wavelength of light emitted by the fluorescent reporter dye once it has been excited and read by the instrument.
    Default Value: Automatic
    Default Calculation: Automatically set to the emission wavelength of the DuplexStainingDye
    Pattern Description: 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers or Null.
    Programmatic Pattern: (qPCREmissionWavelengthP | Automatic) | Null

    ReferenceDyeExcitationWavelength

    The wavelength of light used to excite the fluorescent reference dye.
    Default Value: Automatic
    Default Calculation: Automatically set to the wavelength excitation wavelength of the ReferenceDye
    Pattern Description: 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers or Null.
    Programmatic Pattern: (qPCRExcitationWavelengthP | Automatic) | Null

    ReferenceDyeEmissionWavelength

    The wavelength of light emitted by the fluorescent reference dye once it has been excited and read by the instrument.
    Default Value: Automatic
    Default Calculation: Automatically set to the emission wavelength of the ReferenceDye
    Pattern Description: 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers or Null.
    Programmatic Pattern: (qPCREmissionWavelengthP | Automatic) | Null

    StandardProbeFluorophore

    The fluorescent molecule conjugated to the standard probe that allows for detection of amplification.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Molecule] or Null.
    Programmatic Pattern: (ObjectP[Model[Molecule]] | Automatic) | Null
    Index Matches to: Standard

    StandardProbeExcitationWavelength

    The wavelength of light used to excite the reporter component of the standard probe.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the standard probe.
    Pattern Description: 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers or Null.
    Programmatic Pattern: (qPCRExcitationWavelengthP | Automatic) | Null
    Index Matches to: Standard

    StandardProbeEmissionWavelength

    The wavelength of light emitted by the reporter once it has been excited and read by the instrument.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the standard probe.
    Pattern Description: 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers or Null.
    Programmatic Pattern: (qPCREmissionWavelengthP | Automatic) | Null
    Index Matches to: Standard

    ProbeFluorophore

    The fluorescent molecule conjugated to the probe that allows for detection of amplification.
    Default Value: Automatic
    Default Calculation: Automatically set from the array card model if ArrayCard is True, or Null otherwise.
    Pattern Description: An object of type or subtype Model[Molecule] or list of one or more an object of type or subtype Model[Molecule] entries or Null.
    Programmatic Pattern: ((ObjectP[Model[Molecule]] | {ObjectP[Model[Molecule]]..}) | Automatic) | Null
    Index Matches to: experiment samples

    ProbeExcitationWavelength

    The wavelength of light used to excite the reporter component of the probe.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the probe.
    Pattern Description: 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers or list of one or more 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers entries or Null.
    Programmatic Pattern: ((qPCRExcitationWavelengthP | {qPCRExcitationWavelengthP..}) | Automatic) | Null
    Index Matches to: experiment samples

    ProbeEmissionWavelength

    The wavelength of light emitted by the reporter once it has been excited and read by the instrument.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the probe.
    Pattern Description: 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers or list of one or more 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers entries or Null.
    Programmatic Pattern: ((qPCREmissionWavelengthP | {qPCREmissionWavelengthP..}) | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousProbeFluorophore

    The fluorescent molecule conjugated to the endogenous probe that allows for detection of amplification.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Molecule] or Null.
    Programmatic Pattern: (ObjectP[Model[Molecule]] | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousProbeExcitationWavelength

    The wavelength of light used to excite the reporter component of the endogenous probe.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the endogenous probe.
    Pattern Description: 470 nanometers, 520 nanometers, 550 nanometers, 580 nanometers, 640 nanometers, or 662 nanometers or Null.
    Programmatic Pattern: (qPCRExcitationWavelengthP | Automatic) | Null
    Index Matches to: experiment samples

    EndogenousProbeEmissionWavelength

    The wavelength of light emitted by the reporter once it has been excited and read by the instrument.
    Default Value: Automatic
    Default Calculation: Automatically set to a wavelength appropriate to the fluorophore attached to the endogenous probe.
    Pattern Description: 520 nanometers, 558 nanometers, 586 nanometers, 623 nanometers, 682 nanometers, or 711 nanometers or Null.
    Programmatic Pattern: (qPCREmissionWavelengthP | Automatic) | Null
    Index Matches to: experiment samples

    Standard Curve

    Standard

    The sample that is serially diluted in order to construct a standard curve.
    Default Value: Null
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Model[Sample], Object[Sample]}] | _String) | Null
    Index Matches to: Standard

    StandardPrimerPair

    The primer pair used to amplify a target sequence in Standard.
    Default Value: Null
    Pattern Description: {Forward Primer, Reverse Primer} or {Null, Null} or Null.
    Programmatic Pattern: ({ObjectP[{Model[Sample], Object[Sample]}] | _String, ObjectP[{Model[Sample], Object[Sample]}] | _String} | {Null, Null}) | Null
    Index Matches to: Standard

    SerialDilutionFactor

    The factor by which the standard should be serially diluted with Buffer.
    Default Value: Automatic
    Default Calculation: Resolved automatically to 2, meaning that each standard serial dilution will be twofold.
    Pattern Description: Greater than or equal to 1 and less than or equal to 100 or Null.
    Programmatic Pattern: (RangeP[1, 100] | Automatic) | Null
    Index Matches to: Standard

    NumberOfDilutions

    The number of times the standard should serially diluted, including the original (undiluted) standard sample.
    Default Value: Automatic
    Default Calculation: Resolved automatically to 8, meaning the standard curve will consist of the undiluted standard sample followed by 7 serial dilutions by SerialDilutionFactor.
    Pattern Description: Greater than or equal to 1 and less than or equal to 12 or Null.
    Programmatic Pattern: (RangeP[1, 12] | Automatic) | Null
    Index Matches to: Standard

    NumberOfStandardReplicates

    The number of times the standard should be replicated per each unique set of primer target pairs.
    Default Value: Automatic
    Default Calculation: Resolved automatically to 1.
    Pattern Description: Greater than or equal to 1 and less than or equal to 10 or Null.
    Programmatic Pattern: (RangeP[1, 10] | Automatic) | Null
    Index Matches to: Standard

    StandardForwardPrimerVolume

    The total volume of each forward primer to add to the standard reaction.
    Default Value: Automatic
    Default Calculation: Automatically resolves to match StandardReversePrimerVolume; otherwise, defaults to 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: Standard

    StandardReversePrimerVolume

    The total volume of each reverse primer to add to the standard reaction.
    Default Value: Automatic
    Default Calculation: Automatically resolves to match StandardForwardPrimerVolume; otherwise, defaults to 1 Microliter.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: Standard

    StandardProbe

    The short oligomer strand containing a reporter and quencher, which when separated during the synthesis reaction will result in fluorescence.
    Default Value: Null
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Model[Sample], Object[Sample]}] | _String) | Null
    Index Matches to: Standard

    StandardProbeVolume

    The volume of the standard probe to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 Microliter if a Standard Probe is being used.
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 microliters or Null.
    Programmatic Pattern: (RangeP[0.5*Microliter, 50*Microliter] | Automatic) | Null
    Index Matches to: Standard

    Model Input

    PreparedModelContainer

    Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
    Default Value: Automatic
    Default Calculation: If PreparedModelAmount is set to All and when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
    Pattern Description: An object of type or subtype Model[Container] or Null.
    Programmatic Pattern: (ObjectP[Model[Container]] | Automatic) | Null
    Index Matches to: experiment samples

    PreparedModelAmount

    Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer. When set to All and the input model sample is not preparable, the entire amount of the input model sample that comes from one of the Products is prepared. The selected product must have both Amount and DefaultContainerModel populated, and it must not be a KitProduct. When set to All and the input model is preparable such as water, 1 Milliliter of the input model sample is prepared.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 Milliliter.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Sample Handling

    MoatSize

    Indicates the number of concentric perimeters of wells which should be should be filled with MoatBuffer in order to decrease evaporation from the assay samples during the run.
    Default Value: Automatic
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null

    MoatVolume

    Indicates the volume which should be added to each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to the RecommendedFillVolume of the assay plate if informed, or 75% of the MaxVolume of the assay plate if not, if any other moat options are specified.
    Pattern Description: Greater than 0 microliters or Null.
    Programmatic Pattern: (GreaterP[0*Microliter] | Automatic) | Null

    MoatBuffer

    Indicates the buffer which should be used to fill each moat well.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic) | Null

Sample Prep Options

    Sample Preparation

    PreparatoryUnitOperations

    Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSamplePreparation.
    Default Value: Null
    Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.
    Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

    Preparatory Incubation

    Incubate

    Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    IncubationTemperature

    Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null
    Index Matches to: experiment samples

    IncubationTime

    Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    Mix

    Indicates if this sample should be mixed while incubated, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    MixType

    Indicates the style of motion used to mix the sample, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on the container of the sample and the Mix option.
    Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
    Programmatic Pattern: (MixTypeP | Automatic) | Null
    Index Matches to: experiment samples

    MixUntilDissolved

    Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    MaxIncubationTime

    Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    IncubationInstrument

    The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.
    Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.
    Programmatic Pattern: (ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]] | Automatic) | Null
    Index Matches to: experiment samples

    AnnealingTime

    Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.
    Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotContainer

    The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotDestinationWell

    The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquot

    The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Centrifugation

    Centrifuge

    Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    CentrifugeInstrument

    The centrifuge that will be used to spin the provided samples prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeIntensity

    The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
    Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeTime

    The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Greater than 0 minutes or Null.
    Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeTemperature

    The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotContainer

    The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotDestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquot

    The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Filtering

    Filtration

    Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    FiltrationType

    The type of filtration method that should be used to perform the filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
    Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.
    Programmatic Pattern: (FiltrationTypeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterInstrument

    The instrument that should be used to perform the filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.
    Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null
    Index Matches to: experiment samples

    Filter

    The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.
    Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.
    Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null
    Index Matches to: experiment samples

    FilterMaterial

    The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.
    Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    PrefilterMaterial

    The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
    Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    FilterPoreSize

    The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
    Default Value: Automatic
    Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    PrefilterPoreSize

    The pore size of the filter; all particles larger than this should be removed during the filtration.
    Default Value: Automatic
    Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterSyringe

    The syringe used to force that sample through a filter.
    Default Value: Automatic
    Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    FilterHousing

    The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
    Default Value: Automatic
    Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null
    Index Matches to: experiment samples

    FilterIntensity

    The rotational speed or force at which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
    Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterTime

    The amount of time for which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than 0 minutes or Null.
    Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    FilterTemperature

    The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than or equal to 4 degrees Celsius or Null.
    Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterContainerOut

    The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.
    Default Value: Automatic
    Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.
    Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.
    Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquotDestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or Null.
    Programmatic Pattern: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquotContainer

    The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquot

    The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
    Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    FilterSterile

    Indicates if the filtration of the samples should be done in a sterile environment.
    Default Value: Automatic
    Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    Aliquoting

    Aliquot

    Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).
    Default Value: Automatic
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    AliquotAmount

    The amount of a sample that should be transferred from the input samples into aliquots.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
    Index Matches to: experiment samples

    TargetConcentration

    The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Default Calculation: Automatically calculated based on aliquot and buffer volumes.
    Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.
    Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null
    Index Matches to: experiment samples

    TargetConcentrationAnalyte

    The substance whose final concentration is attained with the TargetConcentration option.
    Default Value: Automatic
    Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.
    Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.
    Programmatic Pattern: (ObjectP[IdentityModelTypes] | Automatic) | Null
    Index Matches to: experiment samples

    AssayVolume

    The desired total volume of the aliquoted sample plus dilution buffer.
    Default Value: Automatic
    Default Calculation: Automatically determined based on Volume and TargetConcentration option values.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null
    Index Matches to: experiment samples

    ConcentratedBuffer

    The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    BufferDilutionFactor

    The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
    Pattern Description: Greater than or equal to 1 or Null.
    Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null
    Index Matches to: experiment samples

    BufferDiluent

    The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    AssayBuffer

    The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.
    Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    AliquotSampleStorageCondition

    The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
    Default Value: Automatic
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null
    Index Matches to: experiment samples

    DestinationWell

    The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
    Default Value: Automatic
    Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
    Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.
    Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

    AliquotContainer

    The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.
    Default Value: Automatic
    Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.
    Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries.
    Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null

    AliquotPreparation

    Indicates the desired scale at which liquid handling used to generate aliquots will occur.
    Default Value: Automatic
    Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
    Pattern Description: Manual or Robotic or Null.
    Programmatic Pattern: (PreparationMethodP | Automatic) | Null

    ConsolidateAliquots

    Indicates if identical aliquots should be prepared in the same container/position.
    Default Value: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null

Protocol Options

    Organizational Information

    Template

    A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
    Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

    Name

    A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
    Default Value: Null
    Pattern Description: A string or Null.
    Programmatic Pattern: _String | Null

    Post Experiment

    MeasureWeight

    Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

    MeasureVolume

    Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

    ImageSample

    Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

Example Calls

    Basics

    To perform a qPCR experiment, simply run:

    Multiplexing

    Both singleplex and multiplex reactions can be performed:

    Master Mix

    A stock solution composed of enzymes (DNA polymerase and optionally reverse transcriptase), dyes, and nucleotides used to amplify target sequence(s) is added to the reaction:

    Duplex Staining Dye

    An intercalating dye may be used to stain DNA duplexes:

    Probe

    Reporter- and quencher-labeled oligomer strands may be used for target detection:

    Standard

    A sample may be serially diluted to generate a standard curve:

    Melting Curve

    A melting curve may be performed at the end of the experiment:

    Array Card

    An array card may be used for the experiment:

Preferred Input Containers

    The ViiA 7 accepts 384-well plates and custom array cards.

Data Processing

    Plot the normalized, baseline-subtracted amplification curve:
    Calculate the quantification cycles:
    Calculate the copy numbers:

Warnings and Errors

    Messages  (78)

    ArrayCardContentsMismatch  (1)

    If using an array card, the number of samples on the input array card must match the number of ForwardPrimers, ReversePrimers, and Probes from the array card model:

    ArrayCardExcessiveVolume  (1)

    If using an array card, the total volume of all components (sample, master mix, buffer) cannot exceed ReactionVolume*48:

    ArrayCardTooManySamples  (1)

    If using an array card, the number of samples cannot exceed 8:

    BufferVolumeMismatch  (1)

    If calculated buffer volume required (reaction volume minus total of all component volumes) does not match specified BufferVolume, an error is thrown:

    CalculatedRampRateOutOfRange  (1)

    If the melting curve ramp rate is calculated based on ramp time and start/end temperature and is out of range, an error is thrown:

    DependentOptionMissing  (1)

    If a standards-related option is specified without Standard being specified, an error is thrown:

    DependentSampleOptionMissing  (1)

    If a probe-related option is specified without Probe being specified, an error is thrown:

    DisabledFeatureOptionSpecified  (4)

    If ReverseTranscription->False and related options are specified, an error is thrown:

    If Activation->False and related options are specified, an error is thrown:

    If PrimerAnnealing->False and related options are specified, an error is thrown:

    If MeltingCurve->False and related options are specified, an error is thrown:

    DiscardedArrayCard  (1)

    If using an array card, the array card cannot be discarded:

    DiscardedSamples  (1)

    If samples are discarded, an error is displayed:

    DuplexStainingDyeSpecifiedWithMultiplex  (1)

    If DuplexStainingDye is specified and there's multiplexing in any sample, an error is thrown:

    DuplicateName  (1)

    If the specified value of the Name option is already in use by another qPCR protocol, an error is thrown:

    DuplicateProbeWavelength  (2)

    If duplicate Ex/Em pairs exist between the probes and endogenous probe for a given sample well, an error is thrown:

    If duplicate Ex/Em pairs exist within the probes for given sample well, an error is thrown:

    EndogenousForwardPrimerStorageConditionMismatch  (1)

    The endogenous forward primer storage condition cannot be specified when EndogenousPrimerPair is Null:

    EndogenousPrimersWithoutProbe  (1)

    If EndogenousPrimerPair is specified without EndogenousProbe, an error is thrown:

    EndogenousProbeStorageConditionMismatch  (1)

    The endogenous probe storage condition cannot be specified when EndogenousProbe is Null:

    EndogenousReversePrimerStorageConditionMismatch  (1)

    The endogenous reverse primer storage condition cannot be specified when EndogenousPrimerPair is Null:

    ExcessiveVolume  (1)

    If total volume of all components does not exceed reaction volume for any of the input samples, an error is thrown:

    ForwardPrimerStorageConditionnMismatch  (1)

    The specified forward primer storage conditions should be the same length as the number of forward primers:

    IncompleteDuplexStainingDyeExcitationEmissionPair  (1)

    If either DuplexStainingDyeExcitationWavelength or DuplexStainingDyeEmissionWavelength is specified and the other is not specified, an error is thrown:

    IncompleteEndogenousProbeExcitationEmissionPair  (1)

    For each sample, if either EndogenousProbeExcitationWavelength or EndogenousProbeEmissionWavelength is specified and the other is not specified, an error is thrown:

    IncompleteProbeExcitationEmissionPair  (1)

    For each sample, if either ProbeExcitationWavelength or ProbeEmissionWavelength is specified and the other is not specified, an error is thrown:

    IncompleteReferenceDyeExcitationEmissionPair  (1)

    If either ReferenceDyeExcitationWavelength or ReferenceDyeEmissionWavelength is specified and the other is not specified, an error is thrown:

    IncompleteStandardProbeExcitationEmissionPair  (1)

    For each sample, if either StandardProbeExcitationWavelength or StandardProbeEmissionWavelength is specified and the other is not specified, an error is thrown:

    InvalidArrayCardDuplexStainingDyeOptions  (1)

    If using an array card, the DuplexStainingDye options cannot be specified:

    InvalidArrayCardEndogenousOptions  (1)

    If using an array card, the Endogenous options cannot be specified:

    InvalidArrayCardMeltingCurveOptions  (1)

    If using an array card, the MeltingCurve options cannot be specified:

    InvalidArrayCardMoatOptions  (1)

    If using an array card, the Moat options cannot be specified:

    InvalidArrayCardReagentOptions  (1)

    If using an array card, the ForwardPrimer, ReversePrimer, and Probe volume and storage condition options cannot be specified:

    InvalidArrayCardReplicateOption  (1)

    If using an array card, the NumberOfReplicates option cannot be specified:

    InvalidArrayCardStandardOptions  (1)

    If using an array card, the Standard options cannot be specified:

    InvalidMeltEndpoints  (1)

    If MeltingCurveStartTemperature is greater than or equal to MeltingCurveEndTemperature, an error is thrown:

    InvalidThermocycler  (1)

    If a non-qPCR-compatible thermocycler is specified, an error is thrown:

    MultiplexingWithoutProbe  (1)

    If multiple primer pairs are supplied for a given sample but Probe is not specified to allow for multiplexing, an error is thrown:

    NullSampleVolume  (4)

    If ProbeVolume is Null while Probe is non-Null, an error is thrown:

    If EndogenousForwardPrimerVolume is Null while EndogenousPrimerPair is non-Null, an error is thrown:

    If EndogenousReversePrimerVolume is Null while EndogenousPrimerPair is non-Null, an error is thrown:

    If EndogenousProbeVolume is Null while EndogenousProbe is non-Null, an error is thrown:

    NullVolume  (3)

    If StandardForwardPrimerVolume is Null while StandardPrimerPair is non-Null, an error is thrown:

    If StandardReversePrimerVolume is Null while StandardPrimerPair is non-Null, an error is thrown:

    If StandardProbeVolume is Null while StandardProbe is non-Null, an error is thrown:

    ObjectDoesNotExist  (14)

    Throw a message if we have a sample that does not exist (name form):

    Throw a message if we have a container that does not exist (name form):

    Throw a message if we have a sample that does not exist (ID form):

    Throw a message if we have a container that does not exist (ID form):

    Throw a message if we have a primer sample model that does not exist (name form):

    Throw a message if we have a primer container that does not exist (name form):

    Throw a message if we have a primer sample that does not exist (ID form):

    Throw a message if we have a container that does not exist (ID form):

    Throw a message if we have a sample that does not exist for an array card qPCR (name form):

    Throw a message if we have a container that does not exist for an array card qPCR (name form):

    Throw a message if we have a sample that does not exist for an array card qPCR (ID form):

    Throw a message if we have a container that does not exist for an array card qPCR (ID form):

    Throw a message if we have an array card that does not exist (name form):

    Throw a message if we have an array card that does not exist (ID form):

    PrimerVolumeLengthError  (2)

    If ForwardPrimerVolume and primer input do not match in length for any given sample, an error is thrown:

    If ReversePrimerVolume and primer input do not match in length for any given sample, an error is thrown:

    ProbeDuplexStainingDyeConflict  (1)

    If Probe is specified for any sample and DuplexStainingDye is specified, an error is thrown:

    ProbeFluorophoreLengthError  (1)

    If ProbeFluorophore and Probe do not match in length for any given sample, an error is thrown:

    ProbeLengthError  (1)

    If Probe is specified for a sample but does not match the length of that sample's primer pair input, an error is thrown:

    ProbeStorageConditionMismatch  (1)

    The specified probe storage conditions should be the same length as the number of probes:

    ProbeVolumeLengthError  (1)

    If ProbeVolume and Probe do not match in length for any given sample, an error is thrown:

    QPCRConflictingStorageConditions  (1)

    If one sample is used multiple times in one experiment, the same storage condition must be given:

    ReversePrimerStorageConditionnMismatch  (1)

    The specified reverse primer storage conditions should be the same length as the number of reverse primers:

    SeparateDyesNotSupported  (1)

    If options are specified that direct addition of separate duplex or reference dyes, a feature flag error message is thrown:

    StandardForwardPrimerStorageConditionMismatch  (1)

    When Standard and StandardPrimerPair are Null, StandardForwardPrimerStorageCondition should also be Null:

    StandardPrimerPairNotAmongInputs  (3)

    If the specified standard primer pair does not appear in the set of input primer pairs, a warning is thrown:

    Standard primers among input primers check passes correctly when given a list of standard primers:

    Standard primers among input primers check fails correctly when given a list of standard primers:

    StandardPrimersRequired  (1)

    If Standard is specified but StandardPrimerPair is not specified, an error is thrown:

    StandardProbeStorageConditionMismatch  (1)

    StandardProbeStorageCondition cannot be specified when Standard is Null:

    StandardReversePrimerStorageConditionMismatch  (1)

    When Standard and StandardPrimerPair are Null, StandardReversePrimerStorageCondition should also be Null:

    StandardStorageConditionMismatch  (1)

    When Standard is Null, StandardStorageCondition should also be Null:

    UnknownMasterMix  (1)

    If the specified MasterMix is not a model pre-evaluated for use in ExperimentqPCR, a warning is thrown to notify the user that default values will be used for fold concentration, dye content, and reverse transcriptase content:

Possible Issues

    Missing Standard Curve for Copy Number Analysis

    A standard curve of quantification cycle vs Log10 copy number is required to determine the initial number of target copies in a sample.
Last modified on Wed 20 Aug 2025 10:10:51

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