ExperimentFragmentAnalysis
ExperimentFragmentAnalysis[Samples]⟹Protocol
generates a Protocol object for running qualitative or quantitative fragment analysis of up to 96 DNA or RNA samples in a single run using an array-based capillary electrophoresis instrument. The nucleic acid analytes are separated based on fragment size as the sample runs while there is an applied electric potential across the capillaries filled with a gel matrix.
Fragment Analysis is an analytical technique to separate and analyze nucleic acid fragments. Samples are electrokinetically injected into a capillary filled with a separation gel along with appropriate markers in parallel to a ladder sample. Voltage is then applied across the capillary and analytes migrate in the gel by their electrophoretic mobility. The capillary is imaged over time (RFU) and the migration of different fragments, relative to a calibrated ladder sample, is tracked. FragmentAnalysis is useful for DNA and RNA quality analysis for a range of applications. These include analysis of small and large DNA fragments, NGS libraries, gDNA, cfDNA, as well as integrity, sizing and quantification analysis of small RNA, total RNA and mRNA vaccines.
Experimental Principles
Figure 1.1: Procedural overview of a Fragment Analysis experiment. Each well of a compatible 96-well plate is filled with either a sample, ladder or blank. Step 1: Samples and ladder(s) are mixed with loading buffers, some of which contain appropriate markers. If applicable, blank(s) are loaded into wells not filled by sample(s) or ladder(s). Step 2: The capillaries are conditioned, by default, with a conditioning solution, followed by the loading of a mixture of separation gel and intercalating dye. A series of optional steps including capillary equilibration, pre-marker rinse, marker injection, pre-sample rinse are then performed, if applicable, prior to loading of samples into the capillaries. Step 3: Samples, Ladder(s) and Blank(s) are loaded into the capillaries at a specified voltage and duration. Step 4: The separation of the different fragments occur via electrophoresis as a specified electric potential is applied across the capillaries and the sample analytes migrate through the capillaries and separated according to fragment size. Step 5: Sample fragments are detected as it crosses the capillary array detection window by a CCD detector. Step 6: Raw data is recorded as relative fluorescence unit (RFU) as a factor of migration time and is subsequently processed to give fragment size analyses of the samples (base pair vs time, nucleotide vs time), sample quality number (DNA quality number, RNA quality number) and simulated gel image of all 96 capillary array lanes.
Instrumentation
Agilent Fragment Analyzer 5300
Figure 2.1.1: Instrument diagram for the Fragment Analyzer 5300 system: The instrument uses a capillary array system, which is an ordered bundle of 96 extremely thin, hollow tubes where analyte electrophoretic separation takes place. The short model Capillaries have a physical total length of 55 cm and an effective length of 33 cm, the length effectively traveled by the fragments prior to detection. The instrument has drawer positions to hold reagents contained in compatible plates, including the sample plate, runnning buffer plate, marker plate, pre-marker rinse buffer plate, pre-sample rinse buffer plate and waste plate. Side compartment positions hold the separation gel and dye mixture as well as the conditioning solution, optional capillary flush solutions, and waste container all connected to a 6-way distribution valve that controls loading into the capillaries or waste. Reagents and samples are incubated at room temperature during preparation shortly before loading into the instrument. The plates are handled by a robotic mobile platform that facilitates automated capillary preparation and sample separation. The capillary array is washed and conditioned by a conditioning solution, by default, with an additional optional capillary flush step. Intercalating dye is mixed with the separation gel and loaded into the capillaries prior to marker or sample injections. While samples are separating, the capillaries are dipped in running buffer and fragments are detected through a detection window by a CCD detector. Raw Data comprise of electropherograms (RFU vs migration time) and is further processed into fragment size analyses (bp vs time or nt vs time) and sample quality number values (DQN or RQN).
Experiment Options
General
Instrument
The array-based capillary electrophoresis instrument used for parallel qualitative or quantitative analysis of nucleic acids via separation based on analyte fragment size of up to 84 samples in a single run.
Pattern Description: An object of type or subtype Model[Instrument, FragmentAnalyzer] or Object[Instrument, FragmentAnalyzer]
Programmatic Pattern: ObjectP[{Model[Instrument, FragmentAnalyzer], Object[Instrument, FragmentAnalyzer]}] | Automatic
NumberOfCapillaries
The number of extremely thin, hollow tubes per bundle in the CapillaryArray used in the course of the experiment. Determines the maximum number of samples ran in parallel in a single injection, including a ladder sample which is recommended for every run.
Default Calculation: If the CapillaryArray is specified, automatically set to the NumberOfCapillaries field of the CapillaryArray option. Otherwise, automatically set based on the number of SamplesIn, Ladders (if specified) and Blank (if specified).
CapillaryArrayLength
The length (Short) of the extremely thin hollow tubes (capillary arrays) that is used by the instrument for analyte separation. Short capillaries have shorter separation run times, as well as improved peak efficiency and sensitivity, but yield lower separation resolution. Long capillaries have longer run times but are ideal if a higher separation resolution is desired. For a Short capillary array, the length from the sample inlet end until the detector window (EffectiveLength) is 33 Centimeter, while the length from the sample inlet until outlet end to the reservoir (TotalLength) is 55 Centimeter. For an illustration, see Figure 2.1.1 under Instrumentation.
CapillaryArray
The ordered bundle of extremely thin, hollow tubes (capillary array) that is used by the instrument for analyte separation. Each CapillaryArray has a specific NumberOfCapillaries (96) which indicates the maximum number of samples that are ran in parallel. Each capillary in the array also has a designated CapillaryArrayLength (Short) which affects the separation run times and resolution. Short capillaries have shorter run times, as well as improved peak efficiency and sensitivity, but yield lower separation resolution, and are used by default. Long capillaries have longer run times but are ideal if a higher separation resolution is desired.
Default Calculation: If NumberOfCapillaries is set to 96, set to Model[Part, CapillaryArray, "96-Capillary Array Short"].
Pattern Description: An object of type or subtype Object[Part, CapillaryArray] or Model[Part, CapillaryArray]
Programmatic Pattern: ObjectP[{Object[Part, CapillaryArray], Model[Part, CapillaryArray]}] | Automatic
AnalysisMethod
The method object that contains a set of option values optimized and recommended by the instrument manufacturer that is used as a template for the parameters of the experiment. If not specified by User, an AnalysisMethod is selected from a list of methods for either standard dsDNA or RNA samples according to a selection criteria based on AnalysisStrategy, CapillaryArrayLength and sample information: type of analyte (DNA or RNA), analyte concentrations (High Sensitiviy (Picogram/Microliter) or Standard Sensitivity (Nanogram/Microliter)) and fragment size range (ReadLength, in base pairs or number of nucleotides) of the sample. For more specialized samples (eg DNA smears, plasmid DNA, cfDNA, NGS libraries, samples for CRISPR/Cas9, genomic DNA), it is recommended that AnalysisMethod is selected and specified. For a selection criteria guide on determining the appropriate AnalysisMethod, refer to Figure 3.1 under AnalysisMethod of Experiment Options. Default option values for each AnalysisMethod, including reagents (SeparationGel, LoadingBuffer, Ladder, Blank, Marker, PreMarkerRinseBuffer, PreSampleRinseBuffer), as well as specific parameters of the experiment categories (eg. Sample Preparation, Capillary Conditioning, Capillary Equilibration, Pre-Marker Rinse, Marker Injection, Pre-Sample Rinse, Sample Injection, Separation) are specified in fields of the various Object[Method, FragmentAnalysis] objects available.
Figure 3.1: The appropriate AnalysisMethod for the sample(s) is selected using the following criteria table. All samples in a single experiment are ideally compatible with a single AnalysisMethod.
Default Calculation: Automatically set to appropriate Object[Method,FragmentAnalysis] based on AnalysisStrategy, CapillaryArrayLength and sample information: type of analyte (equal to TargetAnalyteType field in the AnalysisMethod), analyte concentration (greater than MinTargetConcentration field and less than MaxTargetConcentration field of AnalysisMethod) and fragment size range (MinReadLength greater than or equal to MinTargetReadLength field and MaxReadLength less than or equal to MaxTargetReadLength field of the AnalysisMethod), if available. For a selection criteria guide on determining the appropriate AnalysisMethod, refer to Figure 3.1 under AnalysisMethod of Experiment Options.
Programmatic Pattern: (ObjectP[{Object[Method, FragmentAnalysis]}] | ObjectP[{Object[Method, FragmentAnalysis]}]) | Automatic
PreparedPlate
Indicates if SamplesIn are in an instrument-compatible plate (Model[Container, Plate, "96-well Semi-Skirted PCR Plate for FragmentAnalysis"]) that contain all other necessary components (Ladders, Blanks, LoadingBuffer (if applicable)). If PreparedPlate is True, Ladders and Blanks, if any, are designated by Well Position(s) that contain ladder or blank solutions. All wells contain a solution of least 24 Microliter volume to avoid damage to the capillary array. Prepared plates are directly placed in the sample drawer of the instrument, ready for injection, and does not involve any plate preparation steps. Options including SampleVolume, SampleDiluent, SampleDiluentVolume, SampleLoadingBuffer, SampleLoadingBufferVolume, LadderVolume, LadderLoadingBuffer and LadderLoadingBufferVolume are not applicable and are set to Null.
MaxNumberOfRetries
The maximum number of separation runs that can be performed for contents of the sample plate when the raw data (electropherogram) for a sample or ladder indicates no peak(s) detected as assessed by the lack of any baseline-corrected signal above 100 RFU. For each separation run retry, resources such as SeparationGel, Dye and ConditioningSolution are re-prepared by preparing new solutions in new containers. Plate resources (SamplePlate,RunningBufferPlate,PreMarkerRinseBufferPlate and PreSampleRinseBufferPlate) are re-prepared by moving the contents to a new plate with a newly re-assigned well position for any sample(s)/ladder(s) that are affected, as well as their index-matched counterparts (RunningBuffer, PreMarkerRinseBuffer, PreSampleRinseBuffer). The well re-assignment is to avoid the underperforming capillary array assigned in the previous run. Note that the MarkerPlate is not re-prepared and is used as-is for every retry, if applicable, due to the oil-layer that prevents effective reusability of the transferred components.
NumberOfReplicates
The number of wells each input sample is loaded into. For example {input 1, input 2} with NumberOfReplicates->2 will act like {input 1, input 1, input 2, input 2}.
SampleAnalyteType
The nucleic acid type (DNA or RNA) of the analytes in the sample that are separated based on fragment size.
Default Calculation: Automatically set to the most PolymerType that is either DNA or RNA that can be found under Analytes. If Analytes is not populated, automatically set to the most PolymerType that is either DNA or RNA that can be found under Composition. Otherwise, set to DNA.
MinReadLength
The number (or estimated number) of base pairs or nucleotides of the shortest fragment analyte in the sample.
Default Calculation: Automatically set to the lowest number of base pairs or nucleotides of identity models of PolymerType DNA or RNA under the Composition field of the sample, as determined by SequenceLength. Otherwise, automatically set to Null.
Pattern Description: Greater than or equal to 1 and less than or equal to 60000 in increments of 1 or Null.
MaxReadLength
The number (or estimated number) of base pairs or nucleotides of the longest fragment analyte in the sample.
Default Calculation: Automatically set to the highest number of base pairs or nucleotides of identity models of PolymerType DNA or RNA under the Composition field of the sample, as determined by SequenceLength. Otherwise, automatically set to Null.
Pattern Description: Greater than or equal to 1 and less than or equal to 60000 in increments of 1 or Null.
AnalysisStrategy
The objective of the analysis of the samples. Qualitative performs quality assessment of samples and outputs include gel image, electropherogram, total concentration and sample quality number (DNA Quality Number (DQN) or RNA Quality Number (RQN)). Quantitative performs everything a Qualitative analysis does, with the exception of the default loading buffer added to the sample(s) or ladder(s) containing quantified markers that serve as internal standard and allows measurement analyte concentration with better accuracy than Qualitative methods.
Method Saving
AnalysisMethodName
The name that is given to the Object[Method,FragmentAnalysis] that is generated from options specified in the experiment and is uploaded after the experiment is done. Note that if no AnalysisMethodName is provided, no Object[Method,FragmentAnalysis] is saved.
Sample Preparation
SampleVolume
The volume of sample (after aliquoting, if applicable) that is transferred into the plate, prior to addition of SampleDiluent (if applicable) and SampleLoadingBuffer (if applicable), and before loading into the instrument. Each sample is dispensed from Position A1 onwards (from A1, A2, A3...). If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: If SampleDilution is False, automatically set to the TargetSampleVolume field of the AnalysisMethod. If SampleDilution is True, automatically determined based on the concentration of the first identity model of PolymerType DNA or RNA under Composition, and the MaxTargetMassConcentration field of the AnalysisMethod. Otherwise, automatically set to 2 Microliter. If PreparedPlate is True, automatically set to Null.
Pattern Description: Greater than or equal to 0 microliters and less than or equal to 200 microliters or Null.
SampleDilution
Indicates if SampleDiluent is added to the sample (after aliquoting, if applicable) to reduce the sample concentration prior to addition of the SampleLoadingBuffer and loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to False.
SampleDiluent
The buffer solution added to the sample to reduce the sample concentration prior to addition of the SampleLoadingBuffer and loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: If SampleDilution is set to True, automatically set to Model[Sample, "1x Tris-EDTA (TE) Buffer for ExperimentFragmentAnalysis"]. If PreparedPlate is True OR SampleDilution is set to False, automatically set to Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
SampleDiluentVolume
The volume of buffer solution added to the sample to reduce the sample concentration prior to addition of the SampleLoadingBuffer and loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: If SampleDilution is set to True, automatically determined based on the concentration of the identity models of PolymerType matching SampleAnalyteType under Composition, and the MaxTargetMassConcentration field of the AnalysisMethod. Otherwise, automatically set to the difference between SampleVolume and TargetSampleVolume. If PreparedPlate is True, automatically set to Null.
Pattern Description: Greater than or equal to 0 microliters and less than or equal to 200 microliters or Null.
SampleLoadingBuffer
The solution added to the sample (after aliquoting, if applicable), to either add markers (Quantitative) or further dilute (Qualitative) the sample prior to loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Figure 3.2: Default SampleLoadingBuffer and SampleLoadingBufferVolume for each AnalysisMethod. It is highly recommended that the default loading buffer and volume specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SampleLoadingBuffer field of the AnalysisMethod. If PreparedPlate is True, automatically set to Null. For a list of the default SampleLoadingBuffer for each AnalysisMethod, see Figure 3.2 under SampleLoadingBuffer of Experiment Options.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
SampleLoadingBufferVolume
The volume of SampleLoadingBuffer added to the sample (after aliquoting, if applicable), to either add markers to (Quantitative) or further dilute (Qualitative) the sample prior to loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: Automatically set to the SampleLoadingBufferVolume field of the AnalysisMethod. If PreparedPlate is True, automatically set to Null. For a list of the default SampleLoadingBufferVolume for each AnalysisMethod, see Figure 3.2 under SampleLoadingBuffer of Experiment Options.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 200 microliters or Null.
Ladder
The solution(s) that contain nucleic acids of known lengths used for qualitative or quantitative data analysis. One ladder solution, which is dispensed to Position H12 (for a 96-capillary array), is recommended for each run of the capillary array. If multiple ladders are specified, each ladder is dispensed on the sample plate to occupy successive wells up until Position H12 (for a 96-capillary array). For example, with a 96-capillary array with 3 specified ladders, the first ladder is dispensed to Position H10, the second ladder to Position H11 and the third ladder to position H12. If PreparedPlate is set to True, Ladder is specified as the Well Position(s) the ladder solution(s) has been dispensed to, and are consecutive Well Positions to end in H12 (for example, if there are three ladder solutions in the PreparedPlate, Ladder is set to H10, H11 and H12).
Figure 3.3: Default Ladder and LadderVolume for each AnalysisMethod. It is highly recommended that the default ladder specified in the selected AnalysisMethod is used and dispensed in well H12 of the 96-well sample plate to properly process and analyze experimental data.
Default Calculation: If PreparedPlate is False, automatically set to the Ladder field of the AnalysisMethod and is dispensed to occupy successive wells until Position H12 for a 96-capillary array. If PreparedPlate is True, automatically set to {"H12"} unless Well Position(s) are specified. For a list of the default Ladders for each AnalysisMethod, see Figure 3.3 under Ladder of Experiment Options. At ladder is always required at Position H12.
Programmatic Pattern: (((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Alternatives @@ Flatten[AllWells[NumberOfWells -> 96]]) | Automatic) | Null
LadderVolume
The volume of ladder that is transferred into the plate, prior to addition of LadderLoadingBuffer, and before loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: Automatically set to the LadderVolume field of the AnalysisMethod. If PreparedPlate is True, automatically set to Null. For a list of the default LadderVolume for each AnalysisMethod, see Figure 3.3 under Ladder of Experiment Options.
Pattern Description: Greater than or equal to 0 microliters and less than or equal to 200 microliters or Null.
LadderLoadingBuffer
The solution added to the Ladder, to either add markers to or further dilute the Ladder prior to loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Figure 3.4: Default LadderLoadingBuffer and LadderLoadingBufferVolume for each AnalysisMethod. It is highly recommended that the default loading buffer and volume specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the LadderLoadingBuffer field of the AnalysisMethod. If PreparedPlate is True, automatically set to Null. For a list of the default LadderLoadingBuffer for each AnalysisMethod, see Figure 3.4 under LadderLoadingBuffer of Experiment Options.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
LadderLoadingBufferVolume
The volume of LadderLoadingBuffer added to the Ladder (after aliquoting, if applicable), to either add markers to or further dilute the Ladder prior to loading into the instrument. If PreparedPlate is True, this option is not applicable and is set to Null.
Default Calculation: Automatically set to the LadderLoadingBufferVolume field of the AnalysisMethod. If PreparedPlate is True, automatically set to Null. For a list of the default LoadingBufferVolume for each AnalysisMethod, see Figure 3.4 under LadderLoadingBuffer of Experiment Options.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 200 microliters or Null.
Blank
The solution that is dispensed in the well(s) of the sample plate required to be filled that are not filled by a sample or a ladder. For example, for a run using a 96-capillary array, if there are only 79 samples and 1 ladder, 16 wells are filled with Blank.). Wells filled with Blank each contain a volume equal to the total volume of TargetSampleVolume and LoadingBufferVolume of the AnalysisMethod. If PreparedPlate is set to True, Blank is specified as the Well Position(s) the blank solution(s) have been dispensed to.
Figure 3.5: Default Blank for each AnalysisMethod. It is highly recommended that the default blank specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the Blank field of the AnalysisMethod if there are wells unoccupied by the samples or ladders. If PreparedPlate is True and Blank is not specified, automatically set to Null. For a list of the default Blank for each AnalysisMethod, see Figure 3.5 under Blank of Experiment Options.
Programmatic Pattern: (((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Alternatives @@ Flatten[AllWells[NumberOfWells -> 96]]) | Automatic) | Null
Capillary Conditioning
SeparationGel
The gel reagent that serves as sieving matrix to facilitate the optimal separation of the analyte fragments in each sample by size. Each capillary in the array is flushed with the ConditioningSolution followed by filling with a mixture of the SeparationGel and the Dye prior to sample runs.
Figure 3.6: Default SeparationGel for each AnalysisMethod. It is highly recommended that the default separation gel specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SeparationGel field of the AnalysisMethod. For a list of the default SeparationGel for each AnalysisMethod, see Figure 3.6 under SeparationGel of Experiment Options.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
Dye
The solution of a dye molecule that fluoresces when bound to DNA or RNA fragments in the sample and is used in the detection of the analyte fragments as it passes through the detection window of the capillary. Each capillary in the array is flushed with the ConditioningSolution followed by filling with a mixture of the SeparationGel and the Dye prior to sample runs.
Default Calculation: Automatically set to the Dye field of the AnalysisMethod. The default Dye for most AnalysisMethod is Model[Sample, "Intercalating Dye for ExperimentFragmentAnalysis"]
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
ConditioningSolution
The solution used in the priming of the capillaries before filling with the SeparationGel and Dye prior to a sample run. The flushing of the capillary array with the conditioning solution restores capillary performance and helps maintain the low and reproducible electroosmotic flow for more precise analyte mobilities and migration times by stabilizing buffer pH and background electrolyte levels. This step also acts to flush out unwanted molecules or reagents from previous runs to minimize contamination of samples.
Default Calculation: Automatically set to the ConditioningSolution field of the AnalysisMethod. The default conditioning solution for most AnalysisMethod is Model[Sample, StockSolution, "1X Conditioning Solution for ExperimentFragmentAnalysis"]
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
Capillary Flush
CapillaryFlush
Indicates if an optional CapillaryFlush procedure is performed prior to a sample run. A CapillaryFlush step involves running specified CapillaryFlushSolution(s) through the capillaries and into a Waste Plate. CapillaryFlush is False by default since a capillary conditioning step (which also has the effect of washing the capillaries) is always performed prior to every sample run.
Default Calculation: If NumberOfCapillaries is set to a number between 1 to 3, automatically set to True. Otherwise, set to False.
NumberOfCapillaryFlushes
The number of CapillaryFlush steps that are performed prior to the sample run, where the specified CapillaryFlushSolution for each step runs through the capillaries and into the Waste Plate.
Pattern Description: Greater than or equal to 1 and less than or equal to 3 in increments of 1 or Null.
PrimaryCapillaryFlushSolution
The solution that runs through the capillaries and into the Waste Plate during the first CapillaryFlush step.
Default Calculation: If CapillaryFlush is set to True, automatically set to Model[Sample, StockSolution, "1X Conditioning Solution for ExperimentFragmentAnalysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
PrimaryCapillaryFlushPressure
The positive pressure applied at the capillaries' destination by a high pressure syringe pump that drives the PrimaryCapillaryFlushSolution through the capillaries backwards from the reservoir and into the Waste Plate during the first CapillaryFlush step.
Pattern Description: Greater than or equal to 0.1 pounds‐force per inch squared and less than or equal to 300 pounds‐force per inch squared or Null.
PrimaryCapillaryFlushFlowRate
The flow rate of the PrimaryCapillaryFlushSolution as it runs through the capillaries and into the Waste Plate during the first CapillaryFlush step.
Pattern Description: Greater than or equal to 1 microliter per second and less than or equal to 1000 microliters per second or Null.
PrimaryCapillaryFlushTime
The duration for which the PrimaryCapillaryFlushSolution runs through the capillaries and into the Waste Plate during the first CapillaryFlush step.
Pattern Description: Greater than or equal to 1 minute and less than or equal to 240 minutes or Null.
SecondaryCapillaryFlushSolution
The solution that runs through the capillaries and into the Waste Plate during the second CapillaryFlush step.
Default Calculation: If NumberOfCapillaryFlushes is greater than 1, automatically set to Model[Sample,"Agilent Conditioning Solution for Fragment Analysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
SecondaryCapillaryFlushPressure
The positive pressure applied at the capillaries' destination by a high pressure syringe pump that drives the SecondaryCapillaryFlushSolution through the capillaries backwards from the reservoir and into the Waste Plate during the second CapillaryFlush step.
Pattern Description: Greater than or equal to 1 pound‐force per inch squared and less than or equal to 300 pounds‐force per inch squared or Null.
SecondaryCapillaryFlushFlowRate
The flow rate of the SecondaryCapillaryFlushSolution as it runs through the capillaries and into the Waste Plate during the second CapillaryFlush step.
Default Calculation: If NumberOfCapillaryFlushes is greater than 1, automatically set to 200 Microliter/Second.
Pattern Description: Greater than or equal to 1 microliter per second and less than or equal to 1000 microliters per second or Null.
SecondaryCapillaryFlushTime
The duration for which the SecondaryCapillaryFlushSolution runs through the capillaries and into the Waste Plate during the second CapillaryFlush step.
Default Calculation: If NumberOfCapillaryFlushes is greater than 1, automatically set to 180 Second.
Pattern Description: Greater than or equal to 1 minute and less than or equal to 240 minutes or Null.
TertiaryCapillaryFlushSolution
The solution that runs through the capillaries and into the Waste Plate during the third CapillaryFlush step.
Default Calculation: If NumberOfCapillaryFlushes is 3, automatically set to Model[Sample,"Agilent Conditioning Solution for Fragment Analysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
TertiaryCapillaryFlushPressure
The positive pressure applied at the capillaries' destination by a high pressure syringe pump that drives the TertiaryCapillaryFlushSolution through the capillaries backwards from the reservoir and into the Waste Plate during the third CapillaryFlush step.
Pattern Description: Greater than or equal to 1 pound‐force per inch squared and less than or equal to 300 pounds‐force per inch squared or Null.
TertiaryCapillaryFlushFlowRate
The flow rate of the TertiaryCapillaryFlushSolution as it runs through the capillaries and into the Waste Plate during the third CapillaryFlush step.
Pattern Description: Greater than or equal to 1 microliter per second and less than or equal to 1000 microliters per second or Null.
TertiaryCapillaryFlushTime
The duration for which the TertiaryCapillaryFlushSolution runs through the capillaries and into the Waste Plate during the third CapillaryFlush step.
Pattern Description: Greater than or equal to 1 minute and less than or equal to 240 minutes or Null.
Capillary Equilibration
CapillaryEquilibration
Indicates if a voltage is run through the capillaries as the source tips of the capillaries are immersed in the wells of the RunningBufferPlate in order to prepare the gel inside the capillaries and normalize the electroosmotic flow for more precise analyte mobilities and migration times during separation. If applicable, this is done after the introduction of the SeparationGel and Dye into the capillaries.
Figure 3.7: Default EquilibrationVoltage and EquilibrationTime for each AnalysisMethod. It is highly recommended that CapillaryEquilibration is set to True and default values for capillary equilibration related options specified in the selected AnalysisMethod is used for an optimized run.
PreparedRunningBufferPlate
The pre-prepared 96-well plate which contains the buffer solutions that help conduct current through the gel in the capillaries and facilitates the separation of analyte fragments. The tips of the capillaries are immersed in the wells of the RunningBufferPlate during the CapillaryEquilibration and Separation steps. The contents of the wells matching the well position of the Samples, Ladder(s) and Blank(s) serve as the SampleRunningBuffer, LadderRunningBuffer (if applicable) and BlankRunningBuffer (if applicable). In order for the capillary tips to reach the solution, a minimum volume of 1 Milliliter of buffer solution is required in the each well of the plate and must be in plate model Model[Container, Plate, "96-well 1mL Deep Well Plate (Short) for FragmentAnalysis"].
Pattern Description: An object of type or subtype Object[Container, Plate] or a prepared sample or Null.
SampleRunningBuffer
The buffer solution that contains ions that help conduct current through the gel in the capillaries and facilitates the separation of analyte fragments in the sample. The tips of the capillaries are immersed in the wells of a RunningBufferPlate during the CapillaryEquilibration and Separation steps. If PreparedRunningBufferPlate is not specified, a new 96-well plate that contains the SampleRunningBuffer in the matching WellPosition(s) of the SamplesIn is prepared.
Default Calculation: If PreparedRunningBufferPlate is specified, set to the content(s) of the well matching the well position of the SamplesIn. If PreparedRunningBufferPlate is Null, automatically set to the SampleRunningBuffer field of the AnalysisMethod. Otherwise, automatically set to Model[Sample, StockSolution, "1x Running Buffer for ExperimentFragmentAnalysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample.
LadderRunningBuffer
The buffer solution that contains ions that help conduct current through the gel in the capillaries and facilitates the separation of fragments in the ladder. The tips of the capillaries are immersed in the wells of a RunningBufferPlate during the CapillaryEquilibration and Separation steps. If PreparedRunningBufferPlate is not specified, a new 96-well plate that contains the LadderRunningBuffer in the matching WellPosition(s) of the Ladder is prepared.
Default Calculation: If PreparedRunningBufferPlate is specified and Ladder is not Null, set to the content(s) of the well matching the well position of the Ladder(s). If PreparedRunningBufferPlate is Null and Ladder is not Null, automatically set to the LadderRunningBuffer field of the AnalysisMethod.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
BlankRunningBuffer
The buffer solution that contains ions that help conduct current through the gel in the capillaries that contain the blank. The tips of the capillaries are immersed in the wells of a RunningBufferPlate during the CapillaryEquilibration and Separation steps. If PreparedRunningBufferPlate is not specified, a new 96-well plate that contains the BlankRunningBuffer in the matching WellPosition(s) of the Blank is prepared.
Default Calculation: If PreparedRunningBufferPlate is specified and Blank is not Null, set to the content(s) of the well matching the well position of the Blank(s). If PreparedRunningBufferPlate is Null and Blank is not Null, automatically set to the BlankRunningBuffer field of the AnalysisMethod.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
RunningBufferPlateStorageCondition
The non-default condition under which the RunningBufferPlate is stored after the protocol is completed.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal.
EquilibrationVoltage
The electric potential applied across the capillaries as the capillaries are immersed in the RunningBuffer to condition the gel inside the capillaries and normalize the electroosmotic flow for more precise analyte mobilities and migration times prior to a Pre-Marker Rinse or a Pre-Sample Rinse step.
Default Calculation: If CapillaryEquilibration is set to False, automatically set to Null. If CapillaryEquilibration is set to True and EquilibrationVoltage field of the AnalysisMethod is not Null, set to the EquilibrationVoltage field of the AnalysisMethod. If CapillaryEquilibration is set to True and EquilibrationVoltage field of the AnalysisMethod is Null, set to the 8.0 Kilovolt.
Pattern Description: Greater than or equal to 0 kilovolts and less than or equal to 15 kilovolts or Null.
EquilibrationTime
The duration for which electric potential (EquilibrationVoltage) is applied across the capillaries as the capillaries are immersed in the RunningBuffer to condition the gel inside the capillaries and normalize the electroosmotic flow for more precise analyte mobilities and migration times.
Default Calculation: If CapillaryEquilibration is True and AnalysisMethod is specified, automatically set to the EquilibrationTime field of the AnalysisMethod.
Pattern Description: Greater than or equal to 1 second and less than or equal to 20 minutes or Null.
Pre-Marker Rinse
PreMarkerRinse
Indicates if the tips of the capillaries are rinsed by dipping them in and out of the PreMarkerRinseBuffer contained in the wells of a compatible 96-well plate in order to wash off any previous reagents the capillaries may have come in contact with. This step precedes the MarkerInjection step.
Figure 3.8: Default PreMarkerRinse, PreMarkerRinseBuffer and NumberOfPreMarkerRinses for each AnalysisMethod. It is highly recommended that default values for PreMarkerRinse and related options specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: If the AnalysisMethod is specified, automatically set to the PreMarkerRinse field of the AnalysisMethod. Otherwise, automatically set to False.
NumberOfPreMarkerRinses
The number of dips of the capillary tips in and out of the PreMarkerRinseBuffer contained in the wells of a compatible 96-well plate prior to MarkerInjection in order to wash off any previous reagents the capillaries may have come in contact with. This step precedes the MarkerInjection step.
Default Calculation: If PreMarkerRinse is True, automatically set to the NumberOfPreMarkerRinses field of the AnalysisMethod. If PreMarkerRinse is True and the NumberOfPreMarkerRinses field of the AnalysisMethod is Null, automatically set to 1. If PreMarkerRinse is False, automatically set to Null.
Pattern Description: Greater than or equal to 1 and less than or equal to 20 in increments of 1 or Null.
PreMarkerRinseBuffer
The buffer solution that is used to rinse the capillary tips by dipping them in and out of the PreMarkerRinseBuffer contained in the wells of a compatible 96-well plate in order to wash off any previous reagents the sample capillaries may have come in contact with. This step precedes the MarkerInjection step.
Default Calculation: If PreMarkerRinse is True, automatically set to the PreMarkerRinseBuffer field of the AnalysisMethod. For a list of the default PreMarkerRinseBuffer for each AnalysisMethod, see Figure 3.8 under PreMarkerRinse of Experiment Options.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
PreMarkerRinseBufferPlateStorageCondition
The non-default condition under which the PreMarkerRinseBuffer (contained in the PreMarkerRinseBufferPlate) is stored after the protocol is completed.
Default Calculation: If PreMarkerRinseBuffer is not Null, automatically set to Disposal. Otherwise, set to Null.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Marker Injection
MarkerInjection
Indicates if injection of SampleMarker, LadderMarker (if applicable) and BlankMarker (if applicable) into the capillaries is performed prior to a sample run. SampleMarker, LadderMarker and BlankMarker are solutions contained in a MarkerPlate that contains upper and/or lower marker that elutes at a time corresponding to a known nucleotide size.
Figure 3.9: Default MarkerInjection, Marker (SampleMarker, LadderMarker, BlankMarker), MarkerInjectionTime and MArkerInjectionVoltage for each AnalysisMethod. It is highly recommended that default values for MarkerInjection and related options specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: If the AnalysisMethod is specified, automatically set to the MarkerInjection field of the AnalysisMethod. Otherwise, automatically set to False.
PreparedMarkerPlate
The pre-prepared 96-well plate which contains the marker solutions that contain upper and/or lower marker that elutes at a time corresponding to a known nucleotide size. The contents of the wells matching the well position of the Samples, Ladder(s) and Blank(s) serve as the SampleMarker, LadderMarker (if applicable) and BlankMarker (if applicable). In order for the capillary tips to reach the solution, a minimum volume of 50 Microliter of solution is required in the each well of the plate.
Pattern Description: An object of type or subtype Object[Container, Plate] or a prepared sample or Null.
SampleMarker
The solution that contains upper and/or lower marker that elutes at a time corresponding to a known nucleotide size. Tha SampleMarker is injected into the capillaries during MarkerInjection and runs with the samples during Separation. If PreparedMarkerPlate is not specified, a new 96-well plate that contains the SampleMarker in the matching WellPosition(s) of the SamplesIn is prepared.
Default Calculation: If PreparedMarkerPlate is specified, set to the content(s) of the well matching the WellPosition of the SamplesIn. If PreparedMarkerPlate is Null and MarkerInjection is True, automatically set to the SampleMarker field of the AnalysisMethod, if not Null. If PreparedMarkerPlate is Null and MarkerInjection is True and SampleMarker field of AnalysisMethod is Null, automatically set to Model[Sample, "35 bp and 5000 bp Markers for ExperimentFragmentAnalysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
LadderMarker
The solution that contains upper and/or lower marker that elutes at a time corresponding to a known nucleotide size. Tha LadderMarker is injected into the capillaries during MarkerInjection and runs with the Ladder(s) during Separation. If PreparedMarkerPlate is not specified, a new 96-well plate that contains the LadderMarker in the matching WellPosition(s) of the Ladder(s) is prepared.
Default Calculation: If PreparedMarkerPlate is specified, set to the content(s) of the well matching the WellPosition of the Ladder. If PreparedMarkerPlate is Null, MarkerInjection is True and Ladder is not Null, automatically set to the LadderMarker field of the AnalysisMethod, if not Null. If PreparedMarkerPlate is Null, MarkerInjection is True, Ladder is not Null and LadderMarker field of AnalysisMethod is Null, automatically set to Model[Sample, "100-3000 bp DNA Ladder for ExperimentFragmentAnalysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
BlankMarker
The solution that contains upper and/or lower marker that elutes at a time corresponding to a known nucleotide size. Tha BlankMarker is injected into the capillaries during MarkerInjection and runs with the Blank(s) during Separation. If PreparedMarkerPlate is not specified, a new 96-well plate that contains the BlankMarker in the matching WellPosition(s) of the Blank(s) is prepared.
Default Calculation: If PreparedMarkerPlate is specified, set to the content(s) of the well matching the WellPosition of the Blank. If PreparedMarkerPlate is Null, MarkerInjection is True and Blank is not Null, automatically set to the BlankMarker field of the AnalysisMethod, if not Null. If PreparedMarkerPlate is Null, MarkerInjection is True, Blank is not Null and BlankMarker field of AnalysisMethod is Null, automatically set to Model[Sample, "100-3000 bp DNA Ladder for ExperimentFragmentAnalysis"].
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
MarkerInjectionTime
The duration an electric potential (VoltageInjection) is applied across the capillaries to drive the Marker into the capillaries. In VoltageInjection, the injected volume is proportional to the MarkerInjectionTime. In addition, a short InjectionTime reduces band broadening while a longer InjectionTime can serve to minimize voltage or pressure variability during injection.
Default Calculation: If the AnalysisMethod is specified, automatically set to the MarkerInjectionTime field of the AnalysisMethod. If MarkerInjection is True and AnalysisMethod is not specified, automatically set to 5 Second. For a list of the default MarkerInjectionTime for each AnalysisMethod, see Figure 3.9 under MarkerInjection of Experiment Options.
Pattern Description: Greater than or equal to 1 second and less than or equal to 20 minutes or Null.
MarkerInjectionVoltage
The electric potential applied across the capillaries to drive the Marker forward into the capillaries, from the Marker Plate to the capillary inlet, during the MarkerInjection step. The injected volume is proportional to the MarkerInjectionVoltage, where the higher the MarkerInjectionVoltage, the higher the injected volume. For a list of the default MarkerInjectionVoltage for each AnalysisMethod, see Figure 3.9 under MarkerInjection of Experiment Options.
Default Calculation: If the AnalysisMethod is specified, automatically set to the MarkerInjectionVoltage field of the AnalysisMethod. If MarkerInjection is True, OR AnalysisMethod is not specified, set to 3 Kilovolt.
Pattern Description: Greater than or equal to 0 kilovolts and less than or equal to 149.7 kilovolts or Null.
MarkerPlateStorageCondition
Default Calculation: If SampleMarker, LadderMarker OR BlankMarker is Not Null, automatically set to Refrigerator. Otherwise, set to Null.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Pre-Sample Rinse
PreSampleRinse
Indicates if the tips of the capillaries are rinsed by dipping them in and out of the PreSampleRinseBuffer contained in the wells of a compatible 96-well plate in order to wash off any previous reagents the capillaries may have come in contact with. This step precedes the sampleInjection step.
Figure 3.10: Default PreSampleRinse, PreSampleRinseBuffer and NumberOfPreSampleRinses for each AnalysisMethod. It is highly recommended that default values for PreSampleRinse and related options specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: If the AnalysisMethod is specified, automatically set to the PreSampleRinse field of the AnalysisMethod. Otherwise, automatically set to False.
NumberOfPreSampleRinses
The number of dips of the capillary tips in and out of the PreSampleRinseBuffer contained in the wells of a compatible 96-well plate prior to MarkerInjection in order to wash off any previous reagents the capillaries may have come in contact with. This step precedes the SampleInjection step.
Default Calculation: If PreSampleRinse is True, automatically set to the NumberOfPreSampleRinses field of the AnalysisMethod. If PreSampleRinse is True and the NumberOfPreSampleRinses field of the AnalysisMethod is Null, automatically set to 1. If PreSampleRinse is False, automatically set to Null.
Pattern Description: Greater than or equal to 1 and less than or equal to 20 in increments of 1 or Null.
PreSampleRinseBuffer
The buffer solution that is used to rinse the capillary tips by dipping them in and out of the PreSampleRinseBuffer contained in the wells of a compatible 96-well plate in order to wash off any previous reagents the sample capillaries may have come in contact with. This step precedes the SampleInjection step. The recommended buffer used for rinsing (Tris-EDTA buffer) maintains the ideal pH for nucleic acid solubilization (Tris buffer), as well as protects the analyte from degradation by DNAses/RNAses (EDTA).
Default Calculation: If PreSampleRinse is True, automatically set to the PreSampleRinseBuffer field of the AnalysisMethod. For a list of the default PreSampleRinseBuffer for each AnalysisMethod, see Figure 3.10 under PreSampleRinse of Experiment Options.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
PreSampleRinseBufferPlateStorageCondition
The non-default condition under which the PreSampleRinseBuffer (contained in the Pre-Sample Rinse Plate) is stored after the protocol is completed.
Default Calculation: If PreSampleRinseBuffer is not Null, automatically set to Disposal. Otherwise, set to Null.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Sample Injection
SampleInjectionTime
The duration a electric potential (VoltageInjection) is applied across the capillaries to drive the samples into the capillaries. The injected volume is proportional to the SampleInjectionTime. In addition, a short InjectionTime reduces band broadening while a longer InjectionTime can serve to minimize voltage or pressure variability during injection.
Figure 3.11: Default SampleInjectionTime for each AnalysisMethod. It is highly recommended that the default SampleInjectionTime specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SampleInjectionTime field of the AnalysisMethod. For a list of the default SampleInjectionTime for each AnalysisMethod, see Figure 3.11 under SampleInjectionTime of Experiment Options.
SampleInjectionVoltage
The electric potential applied across the capillaries to drive the samples or ladders forward into the capillaries, from the Sample Plate to the capillary inlet, during the SampleInjection step. The injected volume is proportional to the SampleInjectionVoltage, where the higher the SampleInjectionVoltage, the higher the injected volume.
Figure 3.12: Default SampleInjectionVoltage for each AnalysisMethod. It is highly recommended that the default SampleInjectionVoltage specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SampleInjectionVoltage field of the AnalysisMethod. For a list of the default SampleInjectionVoltage for each AnalysisMethod, see Figure 3.12 under SampleInjectionVoltage of Experiment Options.
Pattern Description: Greater than or equal to 0 kilovolts and less than or equal to 149.7 kilovolts.
Separation
SeparationTime
The duration for which the SeparationVoltage is applied across the capillaries in order for migration of analytes to occur. There should be sufficient SeparationTime for the analytes to migrate from the capillary inlet end to the capillary outlet end for a complete analysis. The higher the SeparationVoltage, the shorter the SeparationTime necessary for complete migration of analytes through the capillaries.
Figure 3.13: Default SeparationTime for each AnalysisMethod. It is highly recommended that the default SeparationTime specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SeparationTime field of the AnalysisMethod. For a list of the default SeparationTime for each AnalysisMethod, see Figure 3.13 under SeparationTime of Experiment Options.
SeparationVoltage
The electric potential applied across the capillaries as the sample analytes migrate through the capillaries during the sample run. Higher SeparationVoltage results in faster separations and higher separation efficiencies but can also cause overheating of sample solutions if set too high.
Figure 3.14: Default SeparationVoltage for each AnalysisMethod. It is highly recommended that the default SeparationVoltage specified in the selected AnalysisMethod is used for an optimized run.
Default Calculation: Automatically set to the SeparationVoltage field of the AnalysisMethod. For a list of the default SeparationVoltage for each AnalysisMethod, see Figure 3.14 under SeparationVoltage of Experiment Options.
Model Input
PreparedModelContainer
Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
PreparedModelAmount
Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer.
Sample Prep Options
Sample Preparation
PreparatoryUnitOperations
Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.
Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.
Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null
PreparatoryPrimitives
Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.
Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.
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 Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
IncubationTemperature
Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
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
IncubationTime
Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
Mix
Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
MixType
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.
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 Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
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 Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
IncubationInstrument
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.
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.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
IncubateAliquotDestinationWell
The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
IncubateAliquot
The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
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.
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 Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
CentrifugeInstrument
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
CentrifugeIntensity
The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
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
CentrifugeTime
CentrifugeTemperature
The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
CentrifugeAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
CentrifugeAliquot
The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
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.
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 Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
FiltrationType
Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
FilterInstrument
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
Filter
The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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
FilterMaterial
The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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, or HLB or Null.
PrefilterMaterial
The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, or HLB or Null.
FilterPoreSize
The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.
Pattern Description: 0.008 micrometers, 0.1 micrometers, 0.2 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.
PrefilterPoreSize
The pore size of the filter; all particles larger than this should be removed during the filtration.
Pattern Description: 0.008 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.
FilterSyringe
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
FilterHousing
The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
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
FilterIntensity
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
FilterTime
Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
FilterTemperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
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 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
FilterAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
FilterAliquot
The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
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.
FilterSterile
Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
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).
AliquotAmount
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.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
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.
TargetConcentrationAnalyte
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.
AssayVolume
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.
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.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
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 Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
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 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.
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 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.
AliquotSampleStorageCondition
The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
DestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
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 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
Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
ConsolidateAliquots
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.
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.
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.
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.
ImageSample
Example Results
- Generate a protocol by specifying a suitable AnalysisMethod where field values of the AnalysisMethod specified are used to populate all Automatic options
- Generate a protocol by specifying MinReadLength and MaxReadLength, which are then used to resolve the AnalysisMethod and consequently, resolve other options
- each data object contains a SimulatedGelImage that gives a summary of fragments detected per well of SamplePlate
- figure below shows the 10 expected bands for sample in Well A1, as well as the 10 expected bands for the ladder in Well H12, while the rest are blanks
- Goal: Prepared a plate of Sample(s), Ladder(s) and Blank(s) and run ExperimentFragmentAnalysis on the plate to separate and identify fragment size of all well contents
- A series of experiments modifying options to properly separate and identify RNA fragments in samples that came from the same source
- Electropherogram Data suggests signal is cut-off and suggests that an extended SeparationTime might be required
- Electropherogram Data now shows all peaks that were originally cut off but with separation quality is still low
- allow Automatic resolution of SeparationGel from the specified AnalysisMethod to see if separation quality is improved
ExperimentFragmentAnalysis[
mySamples,
AnalysisMethod->Object[Method,FragmentAnalysis,"dsDNA (35 -1500 bp) - Standard Sensitivity (ng/uL) - Short"]
]
ExperimentFragmentAnalysis[
mySamples,
MinReadLength->{35,35,35},
MaxReadLength->{1000,1000,1000}
]
Goal:
Confirm the expected fragment sizes in given sample by separation and detection of sample fragments via capillary electrophoresis
myDNASampleModel = Model[Sample,"100-1000 bp DNA Ladder for ExperimentFragmentAnalysis"];
ExperimentFragmentAnalysis[
myDNASampleModel,
AnalysisMethod->Object[Method,FragmentAnalysis,"dsDNA (35 -1500 bp) - Standard Sensitivity (ng/uL) - Short"],
PreparedModelAmount->32 Microliter,
PreparedModelContainer->Model[Container,Vessel,"New 0.5mL Tube with 2mL Tube Skirt"]
]
Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"]
sampleA1Data=Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"][Data][[1]]
peakAnalysisElectropherogram=AnalyzePeaks[sampleA1Data,ReferenceField->Electropherogram];
PlotFragmentAnalysis[sampleA1Data,PrimaryData->Electropherogram,Peaks->peakAnalysisElectropherogram]
peakAnalysisFragmentSize=AnalyzePeaks[sampleA1Data,ReferenceField->DNAFragmentSizeAnalyses];
PlotFragmentAnalysis[sampleA1Data,Peaks->peakAnalysisFragmentSize]
myLadders = Download[Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"],Ladders]
ladderData = Download[Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"],LadderData]
sampleData = Download[Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"],Data];
ladderData = Download[Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"],LadderData];
blankData = ToList[Download[Object[Protocol,FragmentAnalysis,"id:O81aEBvV1OnN"],BlankData][[1]]];
ExperimentFragmentAnalysis[
"sample plate",
AnalysisMethod->Object[Method,FragmentAnalysis,"dsDNA (35 -1500 bp) - Standard Sensitivity (ng/uL) - Short"],
Ladder->"H12",
Blanks->{},
PreparatoryUnitOperations->{
(*series of unit operations for specialized preparation of sample(s), ladder(s) or blank(s)*)
}
]
Object[Protocol,FragmentAnalysis,"id:3em6ZvmP3mov"]
rnaExperiment1=Object[Protocol,FragmentAnalysis,"id:Vrbp1jvBRdGq"]
ExperimentFragmentAnalysis[
myRNASampleModel,
PreparedModelAmount->10 Microliter,
PreparedModelContainer->Model[Container,Vessel,"New 0.5mL Tube with 2mL Tube Skirt"],
AnalysisMethod->Object[Method,FragmentAnalysis,"Small RNA (15 - 200 nt) - High Sensitivity (pg/uL) - Qualitative, Short"],
SeparationGel->Model[Sample,"Separation Gel for ExperimentFragmentAnalysis RNA"]
SeparationTime->60 Minute
]
rnaExperiment2=Object[Protocol,FragmentAnalysis,"id:4pO6dMmlO3oz"]
ExperimentFragmentAnalysis[
myRNASampleModel,
PreparedModelAmount->10 Microliter,
PreparedModelContainer->Model[Container,Vessel,"New 0.5mL Tube with 2mL Tube Skirt"],
AnalysisMethod->Object[Method,FragmentAnalysis,"Small RNA (15 - 200 nt) - High Sensitivity (pg/uL) - Qualitative, Short"]
]
rnaExperiment3=Object[Protocol,FragmentAnalysis,"id:L8kPEjObPMjV"]
Example Calls
Basics
Analyzes the migration of nucleic acid analytes through a separation gel matrix to assess quality and heterogeneity of a sample using a selected AnalysisMethod identified to be optimum for the sample type:
Analyzes the migration of nucleic acid analytes through a separation gel matrix to assess quality and heterogeneity of a sample allowing automatic resolution for optimized options from an optimized AnalysisMethod based on sample composition:
Analyzes samples pre-prepared in an instrument-compatible plate that will not require any sample preparation and is directly loaded into the instrument:
Capillary Flush (Optional)
Perform an additional Capillary Flush step(s) prior to default conditioning and separation run with defined capillary flush related options:
Capillary Equilibration (Optional and Recommended)
Perform capillary equilibration using optimized equilibration option values determined by analysis method:
Perform capillary equilibration using specified equilibration option values overriding values from AnalysisMethod:
Pre-Marker Rinse (Optional)
Marker Injection (applicable only if loading buffers do not already contain markers)
Pre-Sample Rinse (Optional)
Sample Injection and Separation
Preferred Input Containers
The experiment takes common liquid handler compatible containers. PreparedPlate option for SamplePlate and PreparedMarkerPlate requires Model[Container,Plate,"96-well Semi-Skirted PCR Plate for FragmentAnalysis"]. PreparedRunningBufferPlate requires Model[Container,Plate,"96-well 1mL Deep Well Plate (Short) for FragmentAnalysis"]
Warnings and Errors
Messages (76)
AnalysisMethodAnalysisStrategyMismatchWarning (1)
AnalysisMethodBlankMismatch (1)
AnalysisMethodBlankOptionsMismatch (1)
AnalysisMethodLadderMismatch (2)
AnalysisMethodLadderOptionsMismatch (2)
For PreparedPlate is False, if the indicated values for the ladder-related options are not the same as the corresponding field values in the AnalysisMethod, throw a Warning.
For PreparedPlate is True, if the indicated values for the ladder-related options are not the same as the corresponding field values in the AnalysisMethod, throw a Warning.
AnalysisMethodNotOptimized (1)
AnalysisMethodOptionsMismatch (1)
AnalysisMethodSampleOptionsMismatch (2)
For PreparedPlate is False, if the indicated values for the sample-related options are not the same as the corresponding field values in the AnalysisMethod, throw a Warning.
For PreparedPlate is True, if the indicated values for the sample-related options are not the same as the corresponding field values in the AnalysisMethod, throw a Warning.
BlankPreparedPlateMismatchError (2)
BlankRunningBufferMismatchError (2)
CantCalculateSampleDiluentVolume (2)
If the SampleDiluentVolume cannot be calculated (because SampleVolume is Null or not less than target SampleVolume), set to a default value and throw a Warning.
If the SampleDiluentVolume cannot be calculated (because SampleVolume is Null or not less than target SampleVolume), set to a default value and throw a Warning.
CantCalculateSampleVolume (2)
CantDetermineReadLengths (1)
CantDetermineSampleAnalyteType (1)
CapillaryEquilibrationOptionsMismatchErrors (2)
If CapillaryEquilibration is False and any of EquilibrationVoltage and EquilibrationTime is Not Null OR If CapillaryEquilibration is True and any of EquilibrationVoltage and EquilibrationTime is Null, throw an error.
If CapillaryEquilibration is False and any of EquilibrationVoltage and EquilibrationTime is Not Null OR If CapillaryEquilibration is True and any of EquilibrationVoltage and EquilibrationTime is Null, throw an error.
CapillaryFlushNumberOfCapillaryFlushesMismatchError (2)
DuplicateWells (1)
LadderLoadingBufferMismatchError (1)
LadderLoadingBufferVolumeMismatchError (2)
If LadderLoadingBuffer is a specified Object and LadderLoadingBufferVolume is Null or if LadderLoadingBuffer is Null and LadderLoadingBufferVolume is not Null, throw an error.
If LadderLoadingBuffer is a specified Object and LadderLoadingBufferVolume is Null or if LadderLoadingBuffer is Null and LadderLoadingBufferVolume is not Null, throw an error.
LadderMarkerMismatchError (2)
LadderOptionsPreparedPlateMismatchError (1)
LadderPreparedPlateMismatchError (2)
LadderRunningBufferMismatchError (4)
For non-prepared plate, if Ladder is Null and LadderRunningBuffer is specified, throw an error.
For non-prepared plate, if Ladder is specified and LadderRunningBuffer is Null, throw an error.
For prepared plate, if Ladder is Null and LadderRunningBuffer is specified, throw an error.
For prepared plate, If Ladder is specified and LadderRunningBuffer is Null, throw an error.
LadderVolumeMismatchError (2)
MarkerInjectionOptionsMismatchErrors (2)
MarkerInjectionPreparedMarkerPlateMismatchError (1)
MaxLadderVolumeError (1)
MaxSampleVolumeError (2)
NotEnoughSolutionsForInjection (1)
ObjectDoesNotExist (6)
Do NOT throw a message if we have a simulated container but a simulation is specified that indicates that it is simulated:
Do NOT throw a message if we have a simulated sample but a simulation is specified that indicates that it is simulated:
Throw a message if we have a container that does not exist (ID 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 sample that does not exist (name form):
PreMarkerRinseOptionsMismatchErrors (2)
If PreMarkerRinse is False and any of NumberOfPreMarkerRinses, PreMarkerRinseBuffer and PreMarkerRinseBufferPlateStorageCondition is Not Null OR If PreMarkerRinse is True and any of NumberOfPreMarkerRinses, PreMarkerRinseBuffer and PreMarkerRinseBufferPlateStorageCondition is Null, throw an error.
If PreMarkerRinse is False and any of NumberOfPreMarkerRinses, PreMarkerRinseBuffer and PreMarkerRinseBufferPlateStorageCondition is Not Null OR If PreMarkerRinse is True and any of NumberOfPreMarkerRinses, PreMarkerRinseBuffer and PreMarkerRinseBufferPlateStorageCondition is Null, throw an error.
PreparedMarkerPlateError (1)
PreparedMarkerPlateModelError (1)
PreparedPlateAliquotMismatchError (1)
PreparedPlateModelError (1)
PreparedRunningBufferPlateError (1)
PreparedRunningBufferPlateModelError (1)
PreSampleRinseOptionsMismatchErrors (2)
If PreSampleRinse is False and any of NumberOfPreSampleRinses, PreSampleRinseBuffer and PreSampleRinseBufferPlateStorageCondition is Not Null OR If PreSampleRinse is True and any of NumberOfPreSampleRinses, PreSampleRinseBuffer and PreSampleRinseBufferPlateStorageCondition is Null, throw an error.
If PreSampleRinse is False and any of NumberOfPreSampleRinses, PreSampleRinseBuffer and PreSampleRinseBufferPlateStorageCondition is Not Null OR If PreSampleRinse is True and any of NumberOfPreSampleRinses, PreSampleRinseBuffer and PreSampleRinseBufferPlateStorageCondition is Null, throw an error.
PrimaryCapillaryFlushMismatchError (1)
SampleAnalyteTypeAnalysisMethodMismatch (1)
SampleDilutionMismatch (2)
SampleLoadingBufferVolumeMismatchError (2)
SampleOptionsPreparedPlateMismatchError (1)
SecondaryCapillaryFlushMismatchError (1)
TertiaryCapillaryFlushMismatchError (1)
Possible Issues
Optimized options and Incompatible reagents
Optimized experimental parameters and conditions determined by the manufacturer for samples of given criteria are incorporated in different AnalysisMethod(s) (Object[Method,FragmentAnalysis]). Each AnalysisMethod is optimized for given samples based on sample type, fragment size range, and analyte concentration, as well as other specialized sample characteristics. Selection of appropriate AnalysisMethod and using default option values is highly recommended. The use the of the manufacturer recommended reagents, as also defined in the optmized AnalysisMethod, for ConditioningSolution, SeparationGel, Dye, RunningBuffer, Marker, LoadingBuffer, and RinseBuffer is also highly recommended.
CapillaryArray number of uses
Last modified on Wed 7 May 2025 11:44:52