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iLASS Infinium Genotyping Assay v1.0

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Protocol 1: Automated Target Prep (iLASS Infinium Genotyping Assay v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

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Step 1: Select First Workflow Step (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Select First Workflow Step (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

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Automations

chevron-rightSelect First Step v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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Record Details

  • Step Data (Master Step Fields)

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Step 2: Batch DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Batch DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = Standards

  • Derived Sample Generation = Fixed, 1

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Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Same Shape

  • Destination Containers

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Record Details

  • Step Data (Master Step Fields)

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Step 3: Make WGA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name: Make WGA (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

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Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Same Shape

  • Destination Containers

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Record Details

  • Step Data (Master Step Fields)

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Step 4: Make WGA Manual (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Make WGA (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

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Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Same Shape

  • Destination Containers

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Record Details

  • Step Data (Master Step Fields)

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Step 5: Amplify WGA Manual (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Amplify WGA Manual (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

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Automations

chevron-rightSet Next Step - Advance v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Record Details

  • Step Data (Master Step Fields)

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Step 6: Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Fragment DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Instrument Types

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Record Details

  • Step Data (Master Step Fields)

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Step 7: Precipitate DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Precipitate DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Instrument Types

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Record Details

  • Step Data (Master Step Fields)

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Step 8: Resuspend DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Resuspend DNA Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Instrument Types

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Record Details

  • Step Data (Master Step Fields)

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Protocol 2: Automated BeadChip Processing (ILASS Infinium Genotyping Assay v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

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Step 1: Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Hybridize DNA to the BeadChip Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

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Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

  • Destination Containers

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Record Details

  • Step Data (Master Step Fields)

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Step 2: Prepare Hyb Chamber Manual (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Prepare Hyb Chamber Manual (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Reagent Kits

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Automations

chevron-rightSet Next Step - Advance v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Record Details

  • Step Data (Master Step Fields)

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Step 3: Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Wash BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Reagent Kits

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Automations

chevron-rightSet Next Step - Advance v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Record Details

  • Step Data (Master Step Fields)

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Step 4: Extend and Stain BeadChips Automated (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Extend and Stain BeadChips Automated (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Instrument Types

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Record Details

  • Step Data (Master Step Fields)

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Step 5: Wash and Coat BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Wash and Coat BeadChips Manual (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Reagent Kits

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Record Details

  • Step Data (Master Step Fields)

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Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay v1.0)

Protocol Type = Other

Next Steps Configuration

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Step 1: Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

  • Instrument Types

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Automations

chevron-rightSet Next Step - Advance v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Record Details

  • Step Data (Master Step Fields)

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Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay v1.0)

Protocol Type = Sample Prep

Next Steps Configuration

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Step 1: Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.0)

  • Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.0)

  • Step Type = No Outputs

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Automations

chevron-rightStart Analysis v1.0hashtag
  • Trigger Location = Record Details

  • Trigger Style = Manual button

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Record Details

  • Step Data (Master Step Fields)

Step File Placeholders
  • Log - Automatically attached

  • AssayRunLog - Manually uploaded

Instrument Types
  • Hamilton Star

    • Vendor = Hamilton

  • 96 well plate

Step File Placeholders
  • Plate Manifest - Manually uploaded

  • Log - Automatically attached

  • Plate Transfer Plan - Manually uploaded

  • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Plating Source Barcode

      Text

  • Instrument Types
    • Hamilton Star

      • Vendor = Hamilton

  • Reagent Kits

    • AAX-Infinium

      • Supplier = Illumina

    • MA1-Infinium

      • Supplier = Illumina

    • MA2-Infinium

      • Supplier = Illumina

    • 96 well plate

    Plate Transfer Plan

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Container

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Related Source Container

      Text

  • Instrument Types
    • Hamilton Star

      • Vendor = Hamilton

  • Reagent Kits

    • AAX-Infinium

      • Supplier = Illumina

    • MA1-Infinium

      • Supplier = Illumina

    • MA2-Infinium

      • Supplier = Illumina

    • 96 well plate

    Plate Transfer Plan

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Instruction Notes

    Multiline Text

    Read Only

    Default = Incubate the WGA plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      Source DNA Plate Barcode

      Text

  • Tecan EVO
    • Vendor = Tecan

  • Reagent Kits

    • FMS-Infinium

      • Supplier = Illumina

  • Instruction Notes

    Multiline Text

    Read Only

    Plate Transfer Plan

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Tecan EVO
    • Vendor = Tecan

  • Reagent Kits

    • PMX-Infinium

      • Supplier = Illumina

  • Comment

    Multiline Text

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      IsRecombined

      Toggle Switch

  • Tecan EVO
    • Vendor = Tecan

  • Reagent Kits

    • IBX-Infinium

      • Supplier = Illumina

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Instrument Types
    • Tecan EVO

      • Vendor = Tecan

    • Infinium Genotyping Array EX-24

    • Infinium Genotyping Array EX-48

    Plate Transfer Plan

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • PB2-Infinium
    • Supplier = Illumina

    Instruction Notes

    Multiline Text

    Read Only

    Default = Add 400 µl PB2 to the top and bottom wells of each beadchip subchamber in the hybridization chamber.

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • PB1-Infinium
    • Supplier = Illumina

    Instruction Notes

    Multiline Text

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    Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Tecan EVO
    • Vendor = Tecan

  • Reagent Kits

    • ATX-Infinium

      • Supplier = Illumina

    • EML-Infinium

      • Supplier = Illumina

    • LX1-Infinium

      • Supplier = Illumina

    • LX2-Infinium

      • Supplier = Illumina

    • PB1-Infinium

      • Supplier = Illumina

    • STX-Infinium

      • Supplier = Illumina

    • XC3-Infinium

      • Supplier = Illumina

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      IsRecombined

      Toggle Switch

  • PB1-Infinium
    • Supplier = Illumina

  • XC4-Infinium

    • Supplier = Illumina

  • Instruction Notes

    Multiline Text

    Read Only

    Default = Add 310 ml PB1 to the PB1 wash dish. Add 310 ml XC4 to the XC4 wash dish.

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • iScan
    • Vendor = Illumina

    Instrument

    Text

    Read Only

    Instrument Run ID

    Text

    Read Only

    Run Start Time

    Text

    Read Only

    Run Complete Time

    Text

    Read Only

    Run Status

    Text

    Read Only

    Failure Reason

    Text

    Read Only

    Log

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      BeadChip Name

      Text

  • Analysis Start Time

    Text

    Read Only

    Analysis Complete Time

    Text

    Read Only

    Analysis Status

    Text

    Read Only

    Log

    Multiline Text

    Read Only

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table (Global Step Fields)

    • Derived Sample

      Field Name

      Field Type

      Options

      Additional Options and Dropdown Items

      BeadChip Name

      Text

  • Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    First Workflow Step Options

    Text Dropdown

    Required Field

    Presets

    • Run Make WGA Step Manually

    • Run Batch DNA Step on Hamilton

    • Run Make WGA Step on Hamilton

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    100% 2-Propanol Prep Date

    Date

    Batch ID

    Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Batch ID

    Text

    Read Only

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    BeadChip Barcode

    Text

    Read Only

    Instrument Type

    Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Analysis Configuration ID

    Text

    Required Field

    Analysis Run Name

    Text

    Read Only

    Read Only

    Required Field

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:validateSampleCount -min 1 -max 1"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
    script:evaluateDynamicExpression \
    -t false \
    -h false \
    -exp 'nextStep = ::ADVANCE::' \
    -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
    script:evaluateDynamicExpression \
    -t false \
    -h false \
    -exp 'nextStep = ::ADVANCE::' \
    -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
    script:evaluateDynamicExpression \
    -t false \
    -h false \
    -exp 'nextStep = ::ADVANCE::' \
    -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
    script:evaluateDynamicExpression \
    -t false \
    -h false \
    -exp 'nextStep = ::ADVANCE::' \
    -log {compoundOutputFileLuid0}"
    bash -c -l "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
    script:evaluateDynamicExpression \
    -exp 'if( step.::Analysis Run Name::.length()>255 ){ fail( ::Analysis Run Name exceeds maximum length of 255:: )}; if( !step.::Analysis Run Name::.matches(::^(?![wW][fF][rR]\\..*)(^[0-9a-zA-Z-_\\.]*$)::)) { fail( ::Analysis Run Name must consist of only alphanumeric, underscore, hyphen and period characters and cannot start with wfr.:: ) }; ' \
    -log {compoundOutputFileLuid0} \
    -t true \
    && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/iscan-automation.jar \
    script:start_process_analysis -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid0}"

    Plating Source Well

    Text

    Related WGA Container

    Text

    Default = No

    Source DNA Plate Barcode

    Text

    Default = No

    Source DNA Plate Barcode

    Text

    Read Only

    Sample Section

    Text

    Read Only

    Imaging Result

    Text

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    Sample Section

    Text

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    Analysis Result

    Text

    Read Only