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ECL`

ExperimentAgaroseGelElectrophoresis

ExperimentAgaroseGelElectrophoresis[Samples]⟹Protocol

generates a Protocol object to conduct electrophoretic size and charged based separation on input Samples by running them through agarose gels. Experiments can be run analytically to assess composition and purity or preparatively to purify selected bands of material as they run through the gel.

    
Agarose gel electrophoresis is a technique used to separate biological macromolecules in a sample. Samples are placed in individual wells of a gel made from agarose dissolved in a water, then analytes are separated by their electrophoretic mobility as a voltage is applied across the gel. The size, charge, and three-dimensional conformation of a molecule affects its electrophoretic mobility. Shorter analytes migrate across the gel towards the anode faster than longer analytes. Unique analytes are separated into distinct bands on the gel, which can be visualized and isolated. Agarose gel electrophoresis is often used to purify the products of PCR and oligonucleotide restriction reactions.
    

Experimental Principles

    Figure 1.1: Procedural overview of an agarose gel electrophoresis experiment. Step 1: A robotic liquid handler is used to place the Samples and LoadingDye into the LoadingPlate. Step 2: The LoadingPlate is mixed and centrifuged. Step 3: The contents of the LoadingPlate are transferred to the Gels on the robotic electrophoresis rig. Step 4: Voltage is applied across the gel and Analytes in the Samples and LoadingDye are separated based on their electrophoretic mobility. Blue and red fluorescent images are periodically taken of the Gels during this separation. Step 5: In Preparative experiments, SamplesOut are created by extracting Analyte Oligomers of known lengths from each SampleIn.

Instrumentation

    Ranger

    Figure 2.1.1: Instrument diagram for the Ranger system. The electrophoresis rig is on the deck of a specialized robotic liquid handler. Pipette tips attached to a robotic arm are used to move samples from the LoadingPlate to individual wells of the Gels. Eletrophoretic separation occurs by applying a voltage across the Gels on the electrophoresis rig. LED arrays and a CCD camera are used to visualize Analyte bands. The deck is capable of running up to four gels. These gel cassettes are a proprietary form factor optimized for on-deck electrophoresis to interface with the liquid handler's gel positions. As such, typical, commercially available gel formats are incompatible with the deck, and all gels are ordered direct from the instrument manufacturer.
    Figure 2.1.2: Imaging system of the Ranger instrument. Fluorescence imaging is used to visualize Analytes in the Gel. Blue and red light pass through the ExcitationFilters to reach the Gel. Fluorescence emitted by Gel passes through the EmissionFilters and is captured with a CCD Camera.

Experiment Options

    General

    Scale

    The method of gel electrophoresis to run to obtain the separation of samples. If set to Preparative, gel is imaged throughout the run and the target band is collected; if set to Analytical, the gel is only be imaged and no bands are collected.
    Default Value: Automatic
    Default Calculation: Automatically set to Analytical if Gel is set a gel of Model in AnalyticalAgaroseGelP, or Preparative if Gel is set to a gel of Model in PreparativeAgaroseGelP or is unspecified. See the ExperimentAgaroseGelElectrophoresis documentation for a full list of these gels.
    Pattern Description: Preparative, Analytical, or SemiPreparative.
    Programmatic Pattern: PurificationScaleP | Automatic

    AgarosePercentage

    The percent of agarose (w/v) present in the gels used in this experiment.
    Default Value: Automatic
    Default Calculation: Automatically set to be the GelPercentage of the Gel if the Gel option has been specified. Otherwise, this option is set based on the average Length of the longest Model[Molecule,Oligomer] present in each of the input samples' Analytes field (or Composition field if there are no Oligomer Analytes for a given sample). The AgarosePercentage is set to be 3%, 2%, 1.5%, 1%, or 0.5% if the average oligomer length is between 1 and 199 basepairs, between 200 and 399 basepairs, between 400 and 1249 basepairs, between 1250 and 3999 basepairs, or larger than 3999 basepairs, respectively.
    Pattern Description: 0.5 percent, 1 percent, 1.5 percent, 2 percent, or 3 percent.
    Programmatic Pattern: AgarosePercentageP | Automatic

    Gel

    The agarose gel(s) that the input samples are run through.
    Figure 3.1: Available Gels for Analytical and Preparative Experiments
    Default Value: Automatic
    Default Calculation: See the ExperimentAgaroseGelElectrophoresis documentation to see what this is set to depending on the Scale and AgarosePercent options.
    Pattern Description: An object of type or subtype Model[Item, Gel] or Object[Item, Gel] or list of one or more an object of type or subtype Object[Item, Gel] entries.
    Programmatic Pattern: (ObjectP[{Model[Item, Gel], Object[Item, Gel]}] | {ObjectP[Object[Item, Gel]]..}) | Automatic

    Ladder

    The sample or model of ladder to be used as a standard, reference ladder in the Experiment.
    Default Value: Automatic
    Default Calculation: Automatically set to be Null if the Scale is Preparative. If the Scale is Analytical, the option is automatically set to Model[Sample, StockSolution, Standard, "GeneRuler dsDNA 10000-50000 bp, 8 bands, 50 ng/uL"] if the AgarosePercentage is 0.5%, to Model[Sample, StockSolution, Standard, "GeneRuler dsDNA 75-20000 bp, 15 bands, 50 ng/uL"] if the AgarosePercentage is 1% or 1.5%, to Model[Sample, StockSolution, Standard, "GeneRuler dsDNA 25-700 bp, 10 bands, 50 ng/uL"] if the AgarosePercentage is 2%, and to Model[Sample, StockSolution, Standard, "GeneRuler dsDNA 10-300 bp, 11 bands, 50 ng/uL"] if the AgarosePercentage is 3%.
    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

    LadderFrequency

    The frequency a reference ladder will be used on each agarose gel in the Experiment. When First is specified, the ladder will be loaded onto the first well of every gel; When specifying FirstAndLast, the ladder will be loaded before and after samples loaded on every gel.
    Default Value: Automatic
    Default Calculation: Automatically set to be Null if the Scale is Preparative. If the Scale is Analytical, the option is automatically set to FirstAndLast.
    Pattern Description: First or FirstAndLast or Null.
    Programmatic Pattern: ((First | FirstAndLast) | Automatic) | Null

    LadderStorageCondition

    The non-default conditions under which any ladder used by this experiment should be stored after the protocol is completed. If left unset, the ladder will be stored according to their Models' DefaultStorageCondition.
    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

    Instrument

    The electrophoresis instrument used for this experiment.
    Default Value: Model[Instrument, Electrophoresis, Ranger]
    Pattern Description: An object of type or subtype Object[Instrument, Electrophoresis] or Model[Instrument, Electrophoresis]
    Programmatic Pattern: ObjectP[{Object[Instrument, Electrophoresis], Model[Instrument, Electrophoresis]}]

    NumberOfReplicates

    The number of wells each input sample is loaded into. For example {input 1, input 2} with NumberOfReplicates->2 acts like {input 1, input 1, input 2, input 2}.
    Default Value: Null
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: GreaterEqualP[2, 1] | Null

    Loading

    SampleVolume

    The amount of each input sample that is mixed with the LoadingDye before a portion of the mixture (the SampleLoadingVolume) is loaded into the gel.
    Default Value: Automatic
    Default Calculation: Automatically set to 52.8 uL if the Scale is Preparative, or to 10 uL if the Scale is Analytical.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 80 microliters.
    Programmatic Pattern: RangeP[1*Micro*Liter, 80*Micro*Liter] | Automatic
    Index Matches to: experiment samples

    LoadingDye

    The dye(s) that are mixed with the sample and LoadingDilutionBuffer according to the SampleVolume, LoadingDilutionBufferVolume, and LoadingDyeVolume options. The dyes contain Ficoll, SYBR Gold, and a cyanine-labeled DNA sizing reference used to mark the progress of the electrophoresis. Note that while one or two LoadingDyes can be specified, it is recommended to use two dyes for each sample. The only accepted LoadingDye Models are members of AgaroseLoadingDyeP.
    Figure 3.2: Default LoadingDye Selections Based on AgarosePercentage
    Default Value: Automatic
    Default Calculation: Automatically set based on the value of the AgarosePercentage option. See the ExperimentAgaroseGelElectrophoresis documentation to see which dyes are chosen for each percentage.
    Pattern Description: List of one or more an object of type or subtype Model[Sample] or Object[Sample] or a prepared sample entries.
    Programmatic Pattern: {(ObjectP[{Model[Sample], Object[Sample]}] | _String)..} | Automatic
    Index Matches to: experiment samples

    LoadingDyeVolume

    The amount of each LoadingDye that is mixed with the sample and LoadingDilutionBuffer according to the SampleVolume, LoadingDilutionBufferVolume, and LoadingDyeVolume options.
    Default Value: Automatic
    Default Calculation: Automatically set to 0.072 * the MaxWellVolume of the specified Gel if the Scale is Preparative, or 0.1875 * the MaxWellVolume of the specified Gel if the Scale is Analytical.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 10 microliters.
    Programmatic Pattern: RangeP[1*Micro*Liter, 10*Micro*Liter] | Automatic
    Index Matches to: experiment samples

    LoadingDilutionBuffer

    The buffer that is mixed with the sample and LoadingDye according to the SampleVolume, LoadingDilutionBufferVolume, and LoadingDyeVolume options.
    Default Value: Automatic
    Default Calculation: If SampleVolume + (2*LoadingDyeVolume) is less 10 uL when the Scale is Analytical, or less than 60 uL when the Scale is Preparative, automatically set to Model[Sample, StockSolution, "1x TE Buffer"].
    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

    LoadingDilutionBufferVolume

    The amount of LoadingDilutionBuffer that is mixed with the sample and LoadingDye according to the SampleVolume, LoadingDilutionBufferVolume, and LoadingDyeVolume options.
    Default Value: Automatic
    Default Calculation: If SampleVolume + (2*LoadingDyeVolume) is less 10 uL when the Scale is Analytical, or less than 60 uL when the Scale is Preparative, automatically set to the difference between the two values.
    Pattern Description: Greater than or equal to 0 microliters and less than or equal to 80 microliters.
    Programmatic Pattern: RangeP[0*Micro*Liter, 80*Micro*Liter] | Automatic
    Index Matches to: experiment samples

    SampleLoadingVolume

    The volume of the sample and loading dye buffer mixture that is loaded into each gel well.
    Default Value: Automatic
    Default Calculation: Automatically set to 50 Microliter if the Scale is Preparative, and 8 Microliter if the Scale is Analytical.
    Pattern Description: Greater than or equal to 5 microliters and less than or equal to 50 microliters.
    Programmatic Pattern: RangeP[5*Microliter, 50*Microliter] | Automatic

    Collection

    AutomaticPeakDetection

    Indicates if the instrument software detects and collects the largest peak within the PeakDetectionRange when Scale is Preparative. It is recommended to set AutomaticPeakDetection to True when Scale is Preparative.
    Default Value: Automatic
    Default Calculation: The AutomaticPeakDetection is set to Null if the Scale is Analytical. The option is set to False if either the CollectionSize or CollectionWidth options are specified as non-Null values. The option is set to be True if the PeakDetectionRange is set to a non-Null value, or if none of the PeakDetectionRange, CollectionSize, or CollectionWidth options are specified.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    PeakDetectionRange

    The range, in base pairs, between which the instrument software detects and collects the largest peak when Scale is Preparative and AutomaticPeakDetection is True.
    Default Value: Automatic
    Default Calculation: The PeakDetectionRange is set to Null if the Scale is Analytical. The option is set to Null if AutomaticPeakDetection is False. If AutomaticPeakDetection is True, it is set to the range between 75% and 110% of the length of the largest Model[Molecule,Oligomer] present in the input Sample's Analytes field, or in the Composition field if there are no Oligomers in the Analytes field.
    Pattern Description: A span from anything greater than or equal to 1 Basepairs and less than or equal to 20000 Basepairs in increments of 1 Basepairs to anything greater than or equal to 1 Basepairs and less than or equal to 20000 Basepairs in increments of 1 Basepairs or Null.
    Programmatic Pattern: (RangeP[1*BasePair, 20000*BasePair, 1*BasePair] ;; RangeP[1*BasePair, 20000*BasePair, 1*BasePair] | Automatic) | Null
    Index Matches to: experiment samples

    CollectionSize

    The size of the sample to collect after purification in base pairs when Scale is Preparative and AutomaticPeakDetection is False.
    Default Value: Automatic
    Default Calculation: The CollectionSize is set to Null if the Scale is Analytical. The option is set to Null if AutomaticPeakDetection is True. If AutomaticPeakDetection is False, it is set to the length of the largest Model[Molecule,Oligomer] present in the input Sample's Analytes field, or in the Composition field if there are no Oligomers in the Analytes field.
    Pattern Description: Greater than or equal to 1 Basepairs and less than or equal to 20000 Basepairs in increments of 1 Basepairs or Null.
    Programmatic Pattern: (RangeP[1*BasePair, 20000*BasePair, 1*BasePair] | Automatic) | Null
    Index Matches to: experiment samples

    CollectionRange

    The range of the collection area in base pairs when the Scale is Preparative AutomaticPeakDetection is False, and CollectionSize is Null. This instrument manufacturer recommends not specifying this option, as doing so may lead to either low sample recovery, or dilute SamplesOut. It is recommended to only specify the CollectionSize and the ExtractionVolume, if AutomaticPeakDetection is False.
    Default Value: Automatic
    Default Calculation: The CollectionRange is set to Null if the Scale is Analytical. The option is set to Null if AutomaticPeakDetection is True. If AutomaticPeakDetection is False, and the CollectionSize option is set to Null, the CollectionRange is set to the range between 92% and 105% of the length of the largest Model[Molecule,Oligomer] present in the input Sample's Analytes field, or in the Composition field if there are no Oligomers in the Analytes field.
    Pattern Description: A span from anything greater than or equal to 1 Basepairs and less than or equal to 20000 Basepairs in increments of 1 Basepairs to anything greater than or equal to 1 Basepairs and less than or equal to 20000 Basepairs in increments of 1 Basepairs or Null.
    Programmatic Pattern: (RangeP[1*BasePair, 20000*BasePair, 1*BasePair] ;; RangeP[1*BasePair, 20000*BasePair, 1*BasePair] | Automatic) | Null
    Index Matches to: experiment samples

    ExtractionVolume

    The amount of running buffer containing nucleotides of the appropriate size designated by the PeakDetectionRange, CollectionSize, or CollectionRange that is removed from Gel during electrophoretic separation and transferred to DestinationPlate. The ExtractionVolume can affect the sample recovery percentage.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if Scale is Analytical, or to 150 uL if the Scale is Preparative.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 450 microliters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 450*Microliter] | Automatic) | Null

    Separation

    SeparationTime

    The amount of time voltage is applied across the gel (if the Scale is Analytical) or the maximum time voltage is applied in attempt to isolate the sample (if the Scale is Preparative).
    Default Value: Automatic
    Default Calculation: Automatically set to 5000 seconds if the Scale is Preparative, and to 2500 seconds if the Scale is Analytical
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 4 hours.
    Programmatic Pattern: RangeP[Minute, 4*Hour] | Automatic

    DutyCycle

    The maximum percent of the SeparationTime that the 100 Volts is applied across the gel, with a voltage switching frequency of 8 kHz. When Scale is Analytical, the DutyCycle is always constant. When Scale is Preparative, the DutyCycle for individual lanes may be reduced below the set maximum so that bands of the desired size can be extracted from adjacent lanes simultaneously.
    Default Value: Automatic
    Default Calculation: Automatically set to 100% if the AgarosePercentage is 2 or 3%, to 50% if the AgarosePercentage is 1.5 or 1%, and to 35% if the AgarosePercentage is 0.5%.
    Pattern Description: Greater than or equal to 1 percent and less than or equal to 100 percent.
    Programmatic Pattern: RangeP[Percent, 100*Percent] | Automatic

    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, 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

    SamplesOutStorageCondition

    The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.
    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

    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 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: 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

    Scale, AgarosePercentage, and Gel

    One way to specify which type of Gel is used is to specify the Scale and AgarosePercentage Options:
    The Gel Option can explicitly be specified:

    Preparative SamplesOut Extraction Parameters

    The recommended method of specifying the Oligomer of interest to be extracted is by setting the PeakDetectionRange Option - an ExtractionVolume amount of the most abundant peak between this range will be collected:
    A method of specifying the Oligomer of interest to be extracted is by setting the CollectionSize Option - an ExtractionVolume amount of this band will be collected, centered on the CollectionSize:

    Accurate Sizing

    Most accurate sizing is achieved by choosing two LoadingDyes with lengths flanking the Oligomer target of interest

Preferred Input Containers

    The LoadingPlate which is placed on the Ranger can be loaded from all Hamilton robot-compatible containers.

Data Processing

    Plot the SampleElectropherogram generated from a preparative run:

Warnings and Errors

    Messages  (40)

    AgaroseCollectionSizeAndRangeBothNull  (1)

    If the AutomaticPeakDetection option is False, either the CollectionSize or CollecitonRange option must not be Null:

    AgaroseExtractionVolumeScaleMismatch  (1)

    The Scale and ExtractionVolume options must not be in conflict:

    AgaroseGelOptionsMismatch  (1)

    If specified, the Gel must be Agarose and be compatible with the AgarosePercentage and Scale options:

    AgaroseLoadingDilutionBufferMismatch  (1)

    If the LoadingDilutionBuffer option is set to an Object, the LoadingDilutionBufferVolume cannot be 0 uL. Conversely, if the LoadingDilutionBufferVolume is 0 uL, the LoadingDilutionBuffer option must be Null:

    AgaroseLoadingDyeRangeCollectionOptionMismatch  (1)

    Most accurate sizing is achieved when the collection-related Option (PeakDetectionRange, CollecitonSize, or CollectionRange) are within the range of Oligomers present in the LoadingDyes:

    AgaroseSampleLoadingVolumeScaleMismatch  (1)

    The SampleLoadingVolume must be at most 8 uL if the Scale is Analytical:

    ConflictingAgaroseAutomaticPeakDetectionCollectionRangeOptions  (1)

    If the AutomaticPeakDetection option is True, the CollectionRange option must be Null:

    ConflictingAgaroseAutomaticPeakDetectionCollectionSizeOptions  (1)

    If the AutomaticPeakDetection option is True, the CollectionSize option must be Null:

    ConflictingAgaroseAutomaticPeakDetectionRangeOptions  (1)

    If the AutomaticPeakDetection option is True, the PeakDetectionRange option must not be Null. If the AutomaticPeakDetection is False, the PeakDetectionRange option must be Null:

    ConflictingAgaroseAutomaticPeakDetectionScaleOptions  (1)

    If the Scale is Analytical, the AutomaticPeakDetection option must be Null. If the Scale is Preparative, the AutomaticPeakDetection option must be True or False:

    ConflictingAgaroseCollectionRangeScaleOptions  (1)

    If the Scale is Analytical, the CollectionRange option must be Null:

    ConflictingAgaroseCollectionSizeAndRangeOptions  (1)

    If the CollectionSize option is specified as a non-Null value, the CollectionRange option must be Null:

    ConflictingAgaroseCollectionSizeScaleOptions  (1)

    The Scale and CollectionSize options must not be in conflict:

    ConflictingAgarosePeakDetectionRangeCollectionRangeOptions  (1)

    If the PeakDetectionRange option is specified, the CollectionRange option must be Null:

    ConflictingAgarosePeakDetectionRangeScaleOptions  (1)

    If the Scale is Analytical, the PeakDetectionRange option must be Null:

    DiscardedSamples  (1)

    If the provided sample is discarded, an error will be thrown:

    DuplicateAgaroseGelObjects  (1)

    If the Gel input is a list of Objects, each Gel Object in the list must be unique:

    InputContainsTemporalLinks  (1)

    A Warning is thrown if any inputs contain temporal links:

    InvalidAgaroseCollectionRange  (1)

    The CollectionRange option cannot be specified as a Span with the same value listed as the start and the end of the range:

    InvalidAgaroseLadder  (1)

    The Ladder must be Null if the Scale is Preparative, or the Ladder must not be Null if the Scale is Analytical:

    InvalidAgaroseLadderFrequency  (1)

    The LadderFrequency must be Null if the Scale is Preparative, or the Ladder must not be Null if the Scale is Analytical:

    InvalidAgaroseLoadingDye  (1)

    Any specified LoadingDye must be a member of AgaroseLoadingDyeP:

    InvalidAgarosePeakDetectionRange  (1)

    The PeakDetectionRange option cannot be specified as a Span with the same value listed as the start and the end of the range:

    InvalidNumberOfAgaroseGels  (1)

    If the Gel input is an Object or list of Objects, the number of input samples must be compatible with the number of Gels:

    MoreThanOneAgaroseGelModel  (1)

    If the Gel option is supplied as a list of Objects, all must be of the same Model:

    NotEnoughAgaroseSampleToLoad  (1)

    The sum of the SampleVolume, the LoadingDyeVolume times the number of LoadingDyes, and LoadingDilutionBufferVolume must be greater than or equal to the SampleLoadingVolume for each input sample:

    ObjectDoesNotExist  (6)

    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):

    Do NOT throw a message if we have a simulated sample but a simulation is specified that indicates that it is simulated:

    Do NOT throw a message if we have a simulated container but a simulation is specified that indicates that it is simulated:

    OnlyOneAgaroseLoadingDye  (1)

    Most accurate sizing is achieved when there are two LoadingDyes specified for each input sample:

    OverwriteLadderStorageCondition  (1)

    LadderStorageCondition is overwritten and set to Null if a Ladder is not used in an experiment:

    SharedContainerStorageCondition  (1)

    The specified SamplesInStorageCondition is fullfillable for samples sharing the same container:

    TooManyAgaroseInputs  (1)

    A maximum of 48 samples can be run if Scale is Preparative. If Scale is Analytical, the maximum is 92 samples:

    TooManyAgaroseLoadingDyes  (1)

    A maximum of two LoadingDyes can be specified for each input sample:

    UnableToDetermineAgaroseCollectionRange  (1)

    The Components field of the input sample must contain a Structure in order to determine the CollectionRange option:

    UnableToDetermineAgaroseCollectionSize  (1)

    The Components field of the input sample must contain an Oligomer with a Strand or Structure in order to determine the CollectionSize option:

    UnableToDetermineAgarosePeakDetectionRange  (1)

    The Components field of the input sample must contain an Oligomer with a Strand or Structure in order to determine the PeakDetectionRange option:

Possible Issues

    Overloading

    Overloading can lead to inaccurate sizing. The loading capacity for discrete bands of dsDNA varies from 250 ng to 2 ug, depending on both the AgarosePercentage and the oligomer length. Please refer to Section 7.2.1 and Table 7.2.1.1 of Object[Report, Literature, "Ranger Technology User Manual Rev 1.14"] for more detailed information.

    Inaccurate Sizing

    High ionic-strength buffers, such as PCR buffers, can have an impact on the migration rate of DNA oligomers (See lanes 4 and 5). Typically, the calculated size of oligomers will be smaller than expected in such buffers. Please refer to Section 7.7.2 of Object[Report, Literature, "Ranger Technology User Manual Rev 1.14"] for more information on how ionic strength affects sizing. This sizing issue can be mitigated by diluting input samples with water. When the Scale is Preparative, there are multiple ways to specify which band will be isolated. The recommended method is to set AutomaticPeakDetection to True, and to specify the PeakDetectionRange. Doing so will collect the largest (most fluorescent) peak in this region. The default PeakDetectionRange is from 75% to 110% of the size of the band of interest. Another reasonable method is to set AutomaticPeakDetection to False and set the CollectionSize to the size of the band of interest. This method may lead to missing the band of interest in a high ionic strength buffer. It is not recommended to specify the CollectionRange, as doing so may lead to low sample recovery or very dilute recovered sample. For more information about size selection, and how the ExtractionVolume is related, please refer to Section 7.3 of Object[Report, Literature, "Ranger Technology User Manual Rev 1.14"].
Last modified on Wed 8 Oct 2025 12:52:04

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