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ExperimentFluorescenceKinetics

ExperimentFluorescenceKinetics[Samples]⟹Protocol

generates a Protocol for measuring fluorescence of the provided Samples over a period of time.

    
ExperimentFluorescenceKinetics allows reactions to be studied over time. The assay requires fluorescent signal to be generated or quenched when two molecules interact. Typically the fluorescent molecule or quenching molecule is injected simultaneous to data collection. The impact of the injection can then be traced over time. Fluorescent signal will be generated when the sample is excited by light at a specific wavelength. It will then give off light at a lower energy wavelength (the so called emission wavelength). Time resolved fluorescence data can be generated by pausing for ~100µs between sample excitation and fluorescence detection, allowing for increased assay sensitivity and reduction of noise. Using these simple principles and creative experimental design, it's possible to do everything from protein protein interaction studies to live cellular monitoring.
    

Experimental Principles

    Figure 1.1: Procedural overview of a Fluorescence Kinetics experiment. Step 1: Samples are prepared in a reader-compatible shallow well plate. Step 2: Injection lines are cleaned and primed. Step 3: The assay plate is optionally held at a specified temperature. Step 4: Injection samples are dispensed into the assay plate. Step 5: The assay plate is shaken. Step 6: Fluorescence is read over a period of time by repeatedly exciting the sample with a xenon flash lamp. Step 7: Optionally, data may be assessed with AnalyzeKinetics to fit rate constants to the reactions.

Instrumentation

    FLUOstar Omega

    Figure 2.1.1: The Omega is a filter-based instrument. It has two independently spinning filter wheels which can be used to support an arbitrary combination of excitation and emission wavelengths. It has eight filter slots in each wheel and all 8 of these filters can be used in a single experiment - though reading will be sequential. The plate chamber can be headed up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to 4 time points during the run. There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is recommended for most assays, except those that use very fast kinetics.

    CLARIOstar

    Figure 2.2.1: The CLARIOstar is primarily a monochromator-based plate reader and can thus support arbitrary combinations of excitation and emission wavelengths. Up to five wavelength pairs can be read in a single run. The CLARIOstar also has specialty excitation and emission filters which be used for particularly sensitive assays, including TR-FRET. The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to 4 time points during the run. There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is generally recommended for assays except those that use very fast kinetics.

    PHERAstar FS

    Figure 2.3.1: The PHERAstar uses optic modules to package excitation and emission filters into a single package. This means wavelength combinations are restricted to those which already exist in the optic module. Up to five excitation/emission pairs can be recorded in a single experiment. Additionally, the PHERAstar supports dual emission so it's possible to record emission data at 2 different wavelengths simultaneously. The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before and/or during the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples at up to four time points during the run. There are two primary kinetics read modes. It can perform all readings, injections and mixing for a single well before moving onto the next well or it can read in cycles, reading all the assay wells in the plate again and again until the RunTime has been reached. The second mode is recommended for most assays, except those that use very fast kinetics.

Experiment Options

    General

    RunTime

    The length of time over which fluorescence measurements should be made.
    Default Value: 45 minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 24 hours.
    Programmatic Pattern: RangeP[1*Minute, 24*Hour]

    ReadOrder

    Indicates if all measurements and injections should be done for one well before advancing to the next (serial) or in cycles in which each well is read once per cycle (parallel).
    Default Value: Parallel
    Pattern Description: Serial or Parallel.
    Programmatic Pattern: ReadOrderP

    PlateReaderMixSchedule

    Indicates the points at which mixing should occur in the plate reader.
    Default Value: Automatic
    Pattern Description: BeforeReadings, BetweenReadings, or AfterInjections or Null.
    Programmatic Pattern: (MixingScheduleP | Automatic) | Null

    Mode

    The type of fluorescence reading which should be performed.
    Default Value: Automatic
    Pattern Description: Fluorescence or TimeResolvedFluorescence.
    Programmatic Pattern: (Fluorescence | TimeResolvedFluorescence) | Automatic

    WavelengthSelection

    Indicates if the emission and excitation wavelengths should be obtained by filters or monochromators.
    Default Value: Automatic
    Pattern Description: Filters or Monochromators.
    Programmatic Pattern: WavelengthSelectionP | Automatic

    Gain

    The gain which should be applied to the signal reaching the primary detector. This may be specified either as a direct voltage, or as a percentage (which indicates that the gain should be set such that the AdjustmentSample fluoresces at that percentage of the instrument's dynamic range).
    Default Value: Automatic
    Default Calculation: If unspecified defaults to 90% if an adjustment sample is provided or if the instrument can scan the entire plate to determine gain. Otherwise defaults to 2500 Microvolt
    Pattern Description: Greater than or equal to 1 microvolt and less than or equal to 4095 microvolts or greater than or equal to 1 percent and less than or equal to 95 percent.
    Programmatic Pattern: (RangeP[1*Percent, 95*Percent] | RangeP[1*Microvolt, 4095*Microvolt]) | Automatic
    Index Matches to: ExcitationWavelength

    DualEmissionGain

    The gain to apply to the signal reaching the secondary detector. This may be specified either as a direct voltage, or as a percentage relative to the AdjustmentSample option.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 microvolt and less than or equal to 4095 microvolts or greater than or equal to 1 percent and less than or equal to 95 percent or Null.
    Programmatic Pattern: ((RangeP[1*Percent, 95*Percent] | RangeP[1*Microvolt, 4095*Microvolt]) | Automatic) | Null
    Index Matches to: ExcitationWavelength

    DelayTime

    The amount of time which should be allowed to pass after excitation and before fluorescence measurement begins.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 0 microseconds and less than or equal to 8000 microseconds or Null.
    Programmatic Pattern: (RangeP[0*Microsecond, 8000*Microsecond] | Automatic) | Null

    ReadTime

    The amount of time for which the fluorescence measurement reading should occur.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 microsecond and less than or equal to 10000 microseconds or Null.
    Programmatic Pattern: (RangeP[1*Microsecond, 10000*Microsecond] | Automatic) | Null

    AdjustmentSample

    The sample which should be used to perform automatic adjustments of gain and/or focal height values at run time. The focal height will be set so that the highest signal-to-noise ratio can be achieved for the AdjustmentSample. The gain will be set such that the AdjustmentSample fluoresces at the specified percentage of the instrument's dynamic range. When multiple aliquots of the same sample is used in the experiment, an index can be specified to use the desired aliquot for adjustments. When set to FullPlate, all wells of the assay plate are scanned and the well of the highest fluorescence intensity if perform gain and focal height adjustments.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Object[Sample] or a prepared sample or FullPlate or {Index, Sample} or Null.
    Programmatic Pattern: ((FullPlate | (ObjectP[Object[Sample]] | _String) | {RangeP[1, 384, 1], ObjectP[Object[Sample]] | _String}) | Automatic) | Null

    RetainCover

    Indicates if the plate seal or lid on the assay container should not be taken off during measurement to decrease evaporation. When this option is set to True, injections cannot be performed as it's not possible to inject samples through the cover.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    ReadLocation

    Indicates if fluorescence should be measured using an optic above the plate or one below the plate.
    Default Value: Automatic
    Default Calculation: Defaults to Bottom if RetainCover is set to True, otherwise defaults to Top.
    Pattern Description: Top or Bottom.
    Programmatic Pattern: ReadLocationP | Automatic

    Temperature

    The temperature at which the experiment will be performed, if using a plate reader with temperature incubation controls.
    Default Value: Ambient
    Pattern Description: Ambient or greater than or equal to 25 degrees Celsius and less than or equal to 45 degrees Celsius.
    Programmatic Pattern: RangeP[$AmbientTemperature, 45*Celsius] | Ambient

    EquilibrationTime

    The length of time for which the assay plates should equilibrate at the assay temperature in the plate reader before being read.
    Default Value: Automatic
    Default Calculation: Defaults to 0 Second if Temperature is set to Ambient. Otherwise defaults to 5 Minute.
    Pattern Description: Greater than or equal to 0 minutes and less than or equal to 1 hour.
    Programmatic Pattern: RangeP[0*Minute, 1*Hour] | Automatic

    NumberOfReadings

    Number of redundant readings which should be taken by the detector to determine a single averaged fluorescence intensity reading.
    Default Value: 100
    Pattern Description: Greater than or equal to 1 and less than or equal to 200.
    Programmatic Pattern: RangeP[1, 200]

    FocalHeight

    The distance from the bottom of the plate carrier to the focal point. If set to Automatic, the focal height will be adjusted based on the Gain adjustment, which will occur only if the gain values are set to percentages.
    Default Value: Automatic
    Pattern Description: Auto or greater than or equal to 0 millimeters and less than or equal to 25 millimeters or Null.
    Programmatic Pattern: ((RangeP[0*Millimeter, 25*Millimeter] | Auto) | Automatic) | Null

    WorkCell

    Indicates the work cell that this primitive will be run on if Preparation->Robotic.
    Default Value: Automatic
    Default Calculation: Automatically set to STAR if Preparation->Robotic.
    Pattern Description: STAR, bioSTAR, microbioSTAR, or qPix or Null.
    Programmatic Pattern: (WorkCellP | Automatic) | Null

    Preparation

    Indicates if this unit operation is carried out primarily robotically or manually. Manual unit operations are executed by a laboratory operator and robotic unit operations are executed by a liquid handling work cell.
    Default Value: Automatic
    Pattern Description: Manual or Robotic.
    Programmatic Pattern: PreparationMethodP | Automatic

    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

    PrimaryInjectionTime

    The time at which the first round of injections should start.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 seconds or Null.
    Programmatic Pattern: GreaterEqualP[0*Second] | Null

    SecondaryInjectionTime

    The time at which the second round of injections should start.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 seconds or Null.
    Programmatic Pattern: GreaterEqualP[0*Second] | Null

    TertiaryInjectionTime

    The time at which the third round of injections should start.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 seconds or Null.
    Programmatic Pattern: GreaterEqualP[0*Second] | Null

    QuaternaryInjectionTime

    The time at which the fourth round of injections should start.
    Default Value: Null
    Pattern Description: Greater than or equal to 0 seconds or Null.
    Programmatic Pattern: GreaterEqualP[0*Second] | Null

    Optics

    ExcitationWavelength

    The wavelength(s) which should be used to excite fluorescence in the samples.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers.
    Programmatic Pattern: RangeP[320*Nanometer, 740*Nanometer] | Automatic
    Index Matches to: ExcitationWavelength

    EmissionWavelength

    The wavelength(s) at which fluorescence emitted from the sample should be measured.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers.
    Programmatic Pattern: RangeP[320*Nanometer, 740*Nanometer] | Automatic
    Index Matches to: ExcitationWavelength

    DualEmissionWavelength

    The wavelength at which fluorescence emitted from the sample should be measured with the secondary detector (simultaneous to the measurement at the emission wavelength done by the primary detector).
    Default Value: Automatic
    Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers or Null.
    Programmatic Pattern: (RangeP[320*Nanometer, 740*Nanometer] | Automatic) | Null
    Index Matches to: ExcitationWavelength

    Instrument

    The plate reader used to measure fluorescence intensity.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, PlateReader] or Object[Instrument, PlateReader]
    Programmatic Pattern: ObjectP[{Model[Instrument, PlateReader], Object[Instrument, PlateReader]}] | Automatic

    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.
    Figure 3.1: Use the moat options, MoatBuffer, MoatVolume and MoatSize to create an outer ring of wells filled with buffer. This has been shown to decrease evaporation during long reads.
    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

    PrimaryInjectionSample

    The sample to be injected in the first round of injections in order to introduce a time sensitive reagent/sample into the plate before/during fluorescence measurement.
    Default Value: Null
    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) | Null
    Index Matches to: experiment samples

    SecondaryInjectionSample

    The sample to be injected in the second round of injections.
    Default Value: Null
    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) | Null
    Index Matches to: experiment samples

    PrimaryInjectionVolume

    The amount of the primary sample which should be injected in the first round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    SecondaryInjectionVolume

    The amount of the secondary sample which should be injected in the second round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    PrimaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the first round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if primary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    SecondaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the second round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if secondary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    PlateReaderMix

    Indicates if samples should be mixed inside the plate reader chamber.
    Default Value: Automatic
    Default Calculation: Automatically set to True if any other plate reader mix options are specified.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    PlateReaderMixTime

    The amount of time samples should be mixed inside the plate reader chamber.
    Default Value: Automatic
    Default Calculation: Automatically set to 30 second if any other plate reader mix options are specified.
    Pattern Description: Greater than or equal to 1 second and less than or equal to 1 hour or Null.
    Programmatic Pattern: (RangeP[1*Second, 1*Hour] | Automatic) | Null

    PlateReaderMixRate

    The rate at which the plate should be agitated inside the plate reader chamber.
    Default Value: Automatic
    Default Calculation: Automatically set to 700 RPM if any other plate reader mix options are specified.
    Pattern Description: Greater than or equal to 100 revolutions per minute and less than or equal to 700 revolutions per minute or Null.
    Programmatic Pattern: (RangeP[100*RPM, 700*RPM] | Automatic) | Null

    PlateReaderMixMode

    The pattern of motion which should be employed to shake the plate.
    Default Value: Automatic
    Default Calculation: Automatically set to DoubleOrbital if any other plate reader mix options are specified.
    Pattern Description: Orbital, DoubleOrbital, or Linear or Null.
    Programmatic Pattern: (MechanicalShakingP | Automatic) | Null

    ReadDirection

    Indicates the order in which wells should be read by specifying the plate path the instrument should follow when measuring fluorescence.
    Figure 3.2: Use the ReadDirection option to control how the plate reader scans the plate during each read cycle. Choosing a more efficient path will lead to a shorter DetectionInterval. Also note that you may want to consider dripping injectors if you're working with low viscosity injection samples.
    Default Value: Row
    Pattern Description: Row, Column, SerpentineRow, or SerpentineColumn.
    Programmatic Pattern: ReadDirectionP

    InjectionSampleStorageCondition

    The non-default conditions under which any injection samples used by this experiment should be stored after the protocol is completed.
    Default Value: Null
    Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    TertiaryInjectionSample

    The sample to be injected in the third round of injections.
    Default Value: Null
    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) | Null
    Index Matches to: experiment samples

    QuaternaryInjectionSample

    The sample to be injected in the fourth round of injections.
    Default Value: Null
    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) | Null
    Index Matches to: experiment samples

    TertiaryInjectionVolume

    The amount of the tertiary sample which should be injected in the third round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    QuaternaryInjectionVolume

    The amount of the quaternary sample which should be injected in the fourth round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    TertiaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the third round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if tertiary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    QuaternaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the fourth round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if quaternary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    Sampling

    SamplingPattern

    Indicates where in the well measurements are taken.
    Figure 3.3: Ring sampling allows multiple measurements over a band with a specified diameter. The specified number of flashes will be equally divided over the ring and a higher number will yield to increased sampling (as seen in A). The average value of all measurements will be returned as a single data point. Spiral sampling follows the same principle as ring sampling, but covers a larger part of the well as it takes spiraling inward measurements. Again the number of flashes determines if the well is highly sampled (A) or lightly (B). Use Matrix sampling to scan over a NxN grid of points. Note that points on the border of the well will not be measured.
    Default Value: Automatic
    Pattern Description: Matrix, Spiral, Ring, or Center.
    Programmatic Pattern: PlateReaderSamplingP | Automatic

    SamplingDistance

    Indicates the length of the region over which sampling measurements are taken.
    Default Value: Automatic
    Default Calculation: Automatically resolves to Null if SamplingPattern is set to Center otherwise resolves to 80% of the diameter of the well.
    Pattern Description: Greater than or equal to 1 millimeter and less than or equal to 6 millimeters or Null.
    Programmatic Pattern: (RangeP[1*Millimeter, 6*Millimeter] | Automatic) | Null

    SamplingDimension

    Specifies the size of the grid used for Matrix sampling. For example SamplingDimension->5 will scan a 5 x 5 grid.
    Default Value: Automatic
    Default Calculation: If the SamplingPattern is set to Matrix, SamplingDimension will be set to 3.
    Pattern Description: Greater than or equal to 2 and less than or equal to 30 or Null.
    Programmatic Pattern: (RangeP[2, 30] | Automatic) | Null

    Post Experiment

    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, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

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 ExperimentSampleManipulation.
    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

    PreparatoryPrimitives

    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 ExperimentSampleManipulation.
    Default Value: Null
    Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.
    Programmatic Pattern: {SampleManipulationP..} | 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, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB 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, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB 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, 0.1 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, 0.1 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 ConcentrationFactor 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, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, 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 or Null.
    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: False or Null.
    Programmatic Pattern: (False | 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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | 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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | 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: Automatic
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

    Excitation and Emission Wavelengths

    Select a single excitation wavelength to excite the sample and one wavelength at which emitted light should be read:
    Provide a list of excitation and emission wavelengths. Readings will occur sequentially. The sample will be repeatedly excited and then emissions will be read:
    Set the DualEmissionWavelength to simultaneously read two different emission wavelengths:

    Injections

    To specify injections, use the InjectionSample, InjectionVolume, and InjectionTime options. The sample and volume options are index matched to the input samples allowing you to control the wells which receive injections and the volumes of those injections. In the example below, all the input samples will receive the first injection after 20 minutes. At the 40 minute mark the first sample will receive a second injection of 75uL, the second sample will receive 25uL, and the third sample will not receive a second injection:

    Plate Reader Mixing

    The assay plate can be mixed during readings by specifying any of the PlateReaderMix options:

    Gain Setting

    Gain can be set as a percentage of the maximum signal the reader can record:
    Alternatively directly specify the voltage to apply to the PMT. This is generally more helpful in repeat experiments. The gain can be taken from Object[Data, FluorescenceKinetics][Gains]

Preferred Input Containers

    The plate readers can read standard SBS shallow well plates. The experiment will automatically transfer aliquots of your samples into a container of model Model[Container, Plate, "96-well Black Wall Greiner Plate"] if they are not already in compatible containers.
    The plate readers can inject samples from samples in 2mL, 15mL and 50 mL tubes while recording kinetic signal. Use the SamplePreparation option to prepare the injection samples if your samples are not in compatible vessels.

Data Processing

    Plot the data generated from a single trajectory or a combined set of trajectories overlaid into a single plot:
    Determine the kinetic rates of the reaction underlying the data:

Warnings and Errors

    Messages  (64)

    AdjustmentSampleIndex  (1)

    Throws an error if the index of the adjustment sample is higher than the number of times that sample appears:

    AdjustmentSampleRequired  (1)

    The adjustment sample must be supplied if gain is specified as a percentage:

    AdjustmentSampleUnneeded  (2)

    An error will be thrown if an AdjustmentSample was provided but the Gain was supplied as a raw voltage and FocalHeight was set to a distance:

    If the Omega is being used, the AdjustmentSample should only be set if it is being used to determine the gain:

    AmbiguousAdjustmentSample  (1)

    If the adjustment sample appears in the input list multiple times, the first appearance of it will be used:

    BottomReadingAliquotContainer  (1)

    If ReadLocation is set to Bottom, the AliquotContainer must have a Clear bottom:

    CoveredInjections  (1)

    The cover cannot be left on if any injections are being performed:

    CoveredTopRead  (1)

    If the cover is being left on while data is collected bottom reads are recommended:

    DualEmissionGainRequired  (1)

    If a dual emission wavelength is set, the corresponding gain must also be provided:

    DualEmissionGainUnneeded  (1)

    DualEmissionGain cannot be provided if no dual emission wavelength is provided:

    DualEmissionUnavailable  (1)

    DualEmissionWavelength and DualEmissionGain can only be set if the requested plate reader supports dual emission:

    DualEmissionWavelengthUnavailable  (1)

    Throws an error if there are no emission filters which can provide the requested wavelength:

    EmissionWavelengthUnavailable  (1)

    Throws an error if the specified plate reader does not support one of the requested emission wavelengths:

    EmptyContainers  (1)

    All containers provided as input to the experiment must contain samples:

    ExcitationWavelengthUnavailable  (1)

    Throws an error if the specified plate reader does not support one of the requested excitation wavelengths:

    FocalHeightAdjustmentSampleRequired  (1)

    The adjustment sample must be supplied as an object if FocalHeight->Auto:

    FocalHeightUnavailable  (1)

    Only certain plate readers support focal height adjustments:

    GainAdjustmentSampleRequired  (1)

    The adjustment sample must be supplied as an object if gain is specified as a percentage and the plate reader being used cannot adjust by examining the full plate:

    HighWellVolume  (1)

    Throws a warning if the injection will fill the well nearly to the top:

    IncompatibleGains  (1)

    Provided values for the Gain and DualEmissionGain must be in the same units:

    IncompatibleMaterials  (1)

    All injection samples must be compatible with the plate reader tubing:

    InjectionFlowRateRequired  (1)

    Throws an error if the corresponding InjectionFlowRate is set to Null when there are injections:

    InjectionFlowRateUnneeded  (1)

    Throws an error if PrimaryInjectionFlowRate is specified, but there are no injections:

    InputContainsTemporalLinks  (1)

    A Warning is thrown if any inputs or options contain temporal links:

    InstrumentPrecision  (1)

    If the specified option value is more precise than the instrument can support it will be rounded:

    IntegrationTimesRequired  (1)

    DelayTime and ReadTime cannot be set to Null if Mode->TimeResolvedFluorescence:

    IntegrationTimesRequiredTogether  (1)

    DelayTime and ReadTime cannot be set to Null if Mode->TimeResolvedFluorescence:

    IntegrationTimesUnneeded  (1)

    DelayTime and ReadTime only apply if Mode->TimeResolvedFluorescence and should not be specified otherwise:

    IntegrationTimesUnsupported  (1)

    DelayTime and ReadTime cannot be set unless the plate reader is capable of providing time-resolved fluorescence:

    InvalidAdjustmentSample  (1)

    AdjustmentSample must be located within one of the assay plates:

    InvalidAliquotContainer  (1)

    The aliquot container must be supported by the plate reader:

    InvalidWavelengthSelection  (1)

    Only filter-based wavelength selection can be used with time-resolved fluorescence:

    MaxWavelengthsExceeded  (1)

    The number of requested emission wavelengths cannot exceed the max number of readings allowed by the instrument:

    MissingInjectionInformation  (2)

    Throws an error if an injection sample is specified without a corresponding volume:

    Throws an error if an injection volume is specified without a corresponding sample:

    MixingParametersConflict  (1)

    Throw an error if PlateReaderMix cannot be resolved because one mixing parameter was specified and another was set to Null:

    MixingParametersRequired  (1)

    Throws an error if PlateReaderMix->True and PlateReaderMixTime has been set to Null:

    MixingParametersUnneeded  (1)

    Throws an error if PlateReaderMix->False and PlateReaderMixTime has been specified:

    MoatAliquotsRequired  (1)

    Moats are created as part of sample aliquoting. As a result if a moat is requested Aliquot must then be set to True:

    MoatParametersConflict  (1)

    The moat options must all be set to Null or to specific values:

    MoatVolumeOverflow  (1)

    The moat wells cannot be filled beyond the MaxVolume of the container:

    ModeUnavailable  (1)

    An error will be thrown and the function call will return $Failed if the PlateReader option cannot be used because the plate reader does not support fluorescence mode experimental readings:

    NonUniqueName  (1)

    The protocol must be given a unique name:

    NoPlateReader  (2)

    Indicates that none of the possible plate readers can provide the requested emission wavelength while in time-resolved fluorescence mode:

    There is no plate reader which can provide both dual emission and time-resolved fluorescence:

    PlateReaderStowaways  (2)

    Indicates if there are additional samples which weren't sent as an inputs which will be heated while performing the experiment:

    The PlateReaderStowaways warning is only thrown if samples are set to be heated or mixed in the plate reader chamber:

    RepeatedPlateReaderSamples  (1)

    Throws an error if the same sample appears multiple time in the input list, but Aliquot has been set to False so aliquots of the repeated sample cannot be created for the read:

    ReplicateAliquotsRequired  (1)

    Throws an error if replicates are requested, but Aliquot has been set to False so replicate samples cannot be created for the read:

    SamplingCombinationUnavailable  (1)

    SamplingDimension is only supported when SamplingPattern->Matrix:

    SharedContainerStorageCondition  (1)

    The specified storage condition cannot conflict with storage conditions of samples sharing the same container:

    SingleInjectionSampleRequired  (1)

    Only one unique sample can be injected in an injection group:

    SinglePlateRequired  (3)

    Prints a message and returns $Failed if all the samples will not be in a single plate before the read starts:

    Samples can only be aliquoted into a single plate:

    Samples must be aliquoted into a container which is compatible with the plate reader:

    TooManyInjectionSamples  (1)

    No more than 2 unique injection samples can be specified since there are only two syringe pumps on current plate reader hardware:

    TooManyMoatWells  (1)

    Throws an error if more wells are required than are available in the plate. Here the moat requires 64 wells and the samples with replicates require 40 wells:

    TooManyPlateReaderSamples  (1)

    The total number of samples, with replicates included, cannot exceed the number of wells in the aliquot plate:

    UnsupportedInstrumentSamplingPattern  (1)

    The Omega can't sample wells using a Matrix pattern:

    UnsupportedWavelengthSelection  (1)

    The type of wavelength selection must be supported by the requested plate reader:

    WavelengthCombinationUnavailable  (1)

    An error will be thrown if the requested plate reader cannot supply the combination of wavelengths:

    WavelengthsSwapped  (1)

    Indicates an error has likely been made if an emission wavelength is lower than its corresponding excitation wavelength:

    WellOverlap  (1)

    The wells to be used for the moat cannot also be used to hold assay samples:

    WellVolumeExceeded  (1)

    Throws an error if the injections will fill the well past its max volume:

Possible Issues

    High Gain

    If the gain is set too high the instrument detector may hit it's reading limit. Data at this limit is unreliable. Generally it is wise to repeat the experiment with a lower gain. Use myData[PrimaryGain] to see the value used in the current experiment.

    Low Gain

    If the gain is set too low there may be no meaningful signal. If your sample starts fluorescent you may wish to use GainWell->FullPlate to scan over every well in the plate and set Gain to a percentage. With these options the instrument will scan every well and use the one which produces the highest signal to set the gain. It will set it to a value that causes the high fluorescing well to read a value at the given percentage of the detector read limit.

    Evaporation

    During long runs evaporation can cause signal drift over time. Additionally using a high NumberOfReadings can lead to an initial hump while the PMT heats up.

    Slow Injections

    If the injection speed is not sufficient mixing may be inadequate.

    Variable Detection Interval

    The detection interval is determined by the instrument at run time. It depends on the number of wells being read, mixing parameters, the number of multichromatics, and the NumberOfReadings. If the read time is too high this may cause relevant kinetics to be missed. For faster kinetics use ReadOrder -> Serial.
Last modified on Mon 19 Dec 2022 11:25:48
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