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iLASS Infinium Genotyping Assay v1.1

Protocol 1: Target Prep (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Make WGA (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Make WGA (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Instrument Types

    • Hamilton Star

      • Vendor = Hamilton

  • Reagent Kits

    • AAX-Infinium

      • Supplier = Illumina

    • MA1-Infinium

      • Supplier = Illumina

    • MA2-Infinium

      • Supplier = Illumina

Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Same Shape

  • Destination Containers

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Container

Step 2: Amplify WGA (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Amplify WGA (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

Automations

Set Next Step - Advance v1.0

  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

Step 3: Fragment DNA (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Fragment DNA (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Instrument Types

    • Tecan EVO

      • Vendor = Tecan

  • Reagent Kits

    • FMS-Infinium

      • Supplier = Illumina

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

Step 4: Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Precipitate DNA (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Instrument Types

    • Tecan EVO

      • Vendor = Tecan

  • Reagent Kits

    • PM1-Infinium

      • Supplier = Illumina

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

Step 5: Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Resuspend DNA (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Instrument Types

    • Tecan EVO

      • Vendor = Tecan

  • Reagent Kits

    • IHX-Infinium

      • Supplier = Illumina

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

Protocol 2: BeadChip Processing (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Prepare Hyb Chamber (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Reagent Kits

    • PB2-Infinium

      • Supplier = Illumina

Automations

Set Next Step - Advance v1.0

  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

Step 2: Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Hybridize DNA to the BeadChip (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Instrument Types

    • Tecan EVO

      • Vendor = Tecan

Placement = Enabled

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

  • Destination Containers

    • Infinium Genotyping Array EX-24

    * Infinium Genotyping Array EX-48

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

Step 3: Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Wash BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Reagent Kits

    • PB1-Infinium

      • Supplier = Illumina

Automations

Set Next Step - Advance v1.0

  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

Step 4: Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Extend and Stain BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Instrument Types

    • 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

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

Step 5: Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Master Step Name = Wash and Coat BeadChips (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = No Outputs

  • Reagent Kits

    • PB1-Infinium

      • Supplier = Illumina

    • XC4-Infinium

      • Supplier = Illumina

Automations

Set Next Step - Advance v1.0

  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • AssayRunLog - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

Protocol 3: Infinium Array Imaging on iScan (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Other

Next Steps Configuration

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

  • Master Step Name = Image Infinium BeadChip on iScan (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = Analysis

  • Derived Sample Generation = Fixed, 1

  • Instrument Types

    • iScan

      • Vendor = Illumina

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Scan Log - Manually uploaded

    • Run Metrics File - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

    • Measurement

Protocol 4: Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

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

  • Master Step Name = Invoke Infinium Analysis (ILASS Infinium Genotyping Assay v1.1)

  • Step Type = Analysis

  • Derived Sample Generation = Fixed, 1

Automations

Start Analysis v1.0

  • Trigger Location = Record Details

  • Trigger Style = Manual button

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}"

Record Details

  • Step Data (Master Step Fields)

  • Step File Placeholders

    • Log - Automatically attached

    • Analysis Report - Manually uploaded

  • Sample Table (Global Step Fields)

    • Derived Sample

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