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Centrifuge

Centrifuge[Options]⟹UnitOperation

centrifuge samples for a specified period of time and at a specified speed or force.

Centrifuge allows the user to specify samples to be moved to a compatible vial and exposed to high-g conditions imparted by spinning the samples rapidly in a circle in a process called centrifugation. Samples after centrifugation can then be collected and used in further experiments.

Experimental Principles

Figure 1.1: Procedural overview of a centrifugation experiment. Step 1: SamplesIn are transferred to centrifuge-compatible tubes if necessary. Step 2: Centrifuge tubes are loaded into the centrifuge where they are spun at the desired speed for the desired time. Incubation at between -10ÂºC and 40ÂºC is optional. Step 3: Samples are removed from the centrifuge for further use.

Instrumentation

Microfuge 16

Figure 2.1: Samples to be centrifuged are counterbalanced in available centrifuge slots. The centrifuge spins the samples around the axis of the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.

Beckman Coulter Microfuge 20R

Figure 2.2: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.

Eppendorf 5920R

Figure 2.3: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional cooling to prevent a buildup of heat caused by the friction of spinning the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.

Avanti J-15R with JA-10.100 Fixed Angle Rotor

Figure 2.4: Samples to be centrifuged are counterbalanced in available centrifuge rotor slots. The centrifuge spins the rotors around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.

Sorvall X4R Pro-MD

Figure 2.5: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional cooling to prevent a buildup of heat caused by the friction of spinning the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.

Optima XPN 80 Preparative Ultracentrifuge

Figure 2.6: This diagram demonstrates the major components of the instrument (Optima XPN 80 Preparative Ultracentrifuge) include a rotor chamber with motor, a vacuum system, and a temperature sensing and control system.A rotor can be loaded into the chamber and spun by the embedded motor at ultra - high speed.A solid state thermopile in the bottom of the rotor chamber monitors rotor temperature.Meanwhile, a solid state thermoelectric refrigeration and heating system controls the temperature from 0 ℃ to 40 ℃.In order to run the samples at best performance, this instrument requires to pull a vacuum on the rotor chamber.Extremely high spinning speed may cause overheating and high frictional forces, so to avoid sample/instrument damage, ultracentrifuges are equipped with both vacuum and refrigeration systems that reduce friction.To achieve higher vacuum level, the vacuum system composes of two pumps, a diffusion pump and a mechanical vacuum pump.Four types of rotors are compatible with the ultracentrifuge.One of them is a swing - bucket rotor SW 32 Ti.Three of them are fixed - angle rotors : Type 45 Ti, Type 70 Ti, and Type 70.1 Ti.The capacity, maximum speed and application of each rotor are different.SW 32 Ti is commonly used for density gradient centrifugation because the samples are centrifuged along the horizontal direction with less influence from gravity force (i.e., mass).Type 45 Ti is with the highest capacity, while Type 70 Ti and 70.1 Ti are with the highest maximum spinning speed. For each type of the rotor, two identical rotors are available except one is served as cold rotor (stored in refrigerator for experiment under low temperature.

VSpin

Figure 2.7: The VSpin robotic centrifuge has a swinging bucket rotor that can hold two SBS standard plates. Plates can be loaded and spins can be performed fully robotically. This centrifuge is accessible only using RoboticSamplePreparation protocols.

HiG4

Figure 2.8: The HiG4 robotic centrifuge has a swinging bucket rotor that can hold two SBS standard plates. Plates can be loaded and spins can be performed fully robotically. This centrifuge is accessible only using RoboticCellPreparation protocols.

Experiment Options

General

Sample

The samples that should be centrifuged.

Default Value: Null

Pattern Description: Container with Well Position or Model Sample or Sample or Container or Null.

Programmatic Pattern: (ObjectP[{Object[Sample], Object[Container]}] | _String) | {Alternatives @@ Flatten[AllWells[NumberOfWells -> 384]] | LocationPositionP, ObjectP[{Object[Container]}] | _String} | ObjectP[Model[Sample]]

Index Matches to: Sample

SampleLabel

A user defined word or phrase used to identify the samples that are being centrifuged, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string.

Programmatic Pattern: _String | Automatic

Index Matches to: Sample

SampleContainerLabel

A user defined word or phrase used to identify the containers of the samples that are being centrifuged, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string.

Programmatic Pattern: _String | Automatic

Index Matches to: Sample

Instrument

The centrifuge that will be used to spin the provided samples.

Default Value: Automatic

Default Calculation: Automatically set to a centrifuge that can attain the specified intensity, time, temperature, and sterility and (if possible) that is compatible with the sample in its current container.

Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge]

Programmatic Pattern: ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic

Index Matches to: Sample

RotorGeometry

Indicates if the provided samples will be spun at a fixed angle or freely pivot. Unique when Preparation -> Manual.

Default Value: Automatic

Default Calculation: Automatically set to a FixedAngleRotor if more than one rotors are available that fit the intensity and container constraints.

Pattern Description: FixedAngleRotor or SwingingBucketRotor or Null.

Programmatic Pattern: ((Null | RotorGeometryP) | Automatic) | Null

Index Matches to: Sample

RotorAngle

The angle of the samples in the rotor that will be applied to spin the provided samples if ultracentrifuge instrument is selected. Unique when Preparation -> Manual.

Default Value: Automatic

Default Calculation: Automatically set to a rotor that could spin samples at specific angle relative to the axis of rotation.

Pattern Description: Degree23, Degree24, or Degree90 or Null.

Programmatic Pattern: ((Null | RotorAngleP) | Automatic) | Null

Index Matches to: Sample

ChilledRotor

Indicates if the ultracentrifuge rotor is stored in refrigerator between usage thus it is prechilled on loading into the ultracentrifuge. Unique when Preparation -> Manual.

Default Value: Automatic

Default Calculation: Automatically set to true if the ultracentrifuge is utilized at cold temperature.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

Rotor

The centrifuge rotor that will be used to spin the provided samples if ultracentrifuge instrument is selected. Unique when Preparation -> Manual.

Default Value: Automatic

Default Calculation: Automatically set to a rotor that can attain the specified intensity, time, temperature, and sterility and (if possible) fits the sample in its current container.

Pattern Description: An object of type or subtype Model[Container, CentrifugeRotor] or Object[Container, CentrifugeRotor] or a prepared sample or Null.

Programmatic Pattern: ((Null | (ObjectP[{Model[Container, CentrifugeRotor], Object[Container, CentrifugeRotor]}] | _String)) | Automatic) | Null

Index Matches to: Sample

Intensity

The rotational speed or the force that will be applied to the samples by centrifugation.

Default Value: Automatic

Default Calculation: Automatically resolves to one fifth of the maximum rotational rate of the centrifuge, rounded to the nearest attainable centrifuge precision.

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth.

Programmatic Pattern: (GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic

Index Matches to: Sample

Time

The amount of time for which the samples will be centrifuged.

Default Value: 5 minutes

Pattern Description: Greater than 0 minutes.

Programmatic Pattern: GreaterP[0*Minute]

Index Matches to: Sample

Temperature

The temperature at which the centrifuge chamber will be held while the samples are being centrifuged.

Default Value: Automatic

Default Calculation: Automatically set to 4 Celsius if ChilledRotor option is set to True.

Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius.

Programmatic Pattern: (Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic

Index Matches to: Sample

CollectionContainer

The container that will be stacked on the bottom of the sample's container to collect the filtrate passing through the filter container.

Default Value: Automatic

Default Calculation: Automatically set to Model[Container, Plate, "96-well 2mL Deep Well Plate"] if the sample is in a filter plate.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Programmatic Pattern: ((Null | ((ObjectP[{Model[Container], Object[Container]}] | _String) | {Alternatives[GreaterEqualP[1, 1]], (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic})) | Automatic) | Null

Index Matches to: Sample

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

WorkCell

The automated workstation with a collection of integrated instruments on which this unit operation will be will be performed if Preparation -> Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, or microbioSTAR or Null.

Programmatic Pattern: ((STAR | bioSTAR | microbioSTAR) | Automatic) | Null

Sterile

Indicates if the protocol should be performed in a sterile environment.

Default Value: Automatic

Pattern Description: True or False.

Programmatic Pattern: BooleanP | 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: (Null | (Alternatives[SampleStorageTypeP | Disposal])) | Null

Index Matches to: Sample

Protocol

NumberOfReplicates

Number of times each of the input samples will be centrifuged using identical experimental parameters.

Default Value: Null

Pattern Description: Greater than or equal to 1 in increments of 1 or Null.

Programmatic Pattern: GreaterEqualP[1, 1] | Null

Sample Prep Options

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: Sample

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: ((Null | (Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature])) | Automatic) | Null

Index Matches to: Sample

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: ((Null | RangeP[1*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | MixTypeP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | RangeP[1*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | RangeP[0*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic})) | Automatic) | Null

Index Matches to: Sample

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: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (RangeP[1*Microliter, 20*Liter] | All)) | Automatic) | Null

Index Matches to: Sample

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: Sample

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: ((Null | FiltrationTypeP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | 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: Sample

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: ((Null | ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | FilterMembraneMaterialP) | Automatic) | Null

Index Matches to: Sample

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.

Programmatic Pattern: ((Null | FilterMembraneMaterialP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | FilterSizeP) | Automatic) | Null

Index Matches to: Sample

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.

Programmatic Pattern: ((Null | FilterSizeP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String)) | Automatic) | Null

Index Matches to: Sample

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: ((Null | ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration])) | Automatic) | Null

Index Matches to: Sample

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: ((Null | GreaterP[0*Minute]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (Alternatives[GreaterEqualP[4*Celsius]])) | Automatic) | Null

Index Matches to: Sample

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: ((Null | ((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic})) | Automatic) | Null

Index Matches to: Sample

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: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic})) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (RangeP[1*Microliter, 20*Liter] | All)) | Automatic) | Null

Index Matches to: Sample

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: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

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: Sample

AliquotSampleLabel

A user defined word or phrase used to identify the samples after they are aliquotted, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

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.

Index Matches to: Sample

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: ((Null | (GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)])) | Automatic) | Null

Index Matches to: Sample

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: ((Null | ObjectP[IdentityModelTypes]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | RangeP[1*Microliter, 20*Liter]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

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: ((Null | GreaterEqualP[1]) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

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: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

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

Programmatic Pattern: ((Null | (SampleStorageTypeP | Disposal)) | Automatic) | Null

Index Matches to: Sample

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

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

Basics

Centrifuge mySamples:

Centrifuge mySamples in specified instrument:

Centrifuge mySamples with custom parameters:

Centrifuge mySamples in a sterile instrument:

Centrifuge mySamples in ultracentrifuge with a specified rotor:

Preferred Input Containers

Containers that are compatible with the Microfuge 16 model centrifuge.

Containers that are compatible with the Microfuge 20R model centrifuge.

Containers that are compatible with the Optima XPN80 model centrifuge.

Some examples of SBS plates that are compatible with Agilent VSpin robotic centrifuge (ExperimentRoboticSamplePreparation only).

Some examples of SBS plates that are compatible with the BioNex HiG4 robotic centrifuge (ExperimentRoboticCellPreparation only).

Warnings and Errors

Messages

Possible Issues

Microfuge 16 temperature is not controlled

The Microfuge 16 centrifuge is unable to control its internal temperature. If extended centrifuge times are called, the SamplesIn may be heated to an undesirable temperature. If this may be a concern, please investigate using the Microfuge 20R instrument, which may be refrigerated.

BioNex HiG4 centrifuge requires skirted plates

The BioNex HiG4 rotor bucket is equipped with a pedestal to support skirted plates during high intensity spinning. If plates with short or no skirt are used in this centrifuge, they may not be effectively retained and may fall out of the bucket during spinning. Please make sure that the skirt of your plate is longer than 1.2 mm.

Last modified on Fri 3 Oct 2025 18:27:58