Infinium HTS Assay Manual v1.2

Overview

The Infinium HTS Assay Manual workflow includes the following functionality.

• Preconfigured Infinium HTS Assay Manual protocols.

• Automatic placement of samples when necessary.

• Automatic step transition when required.

• Automatic calculation or display of reagents at every step in the protocol.

Protocol 1: Prep Sample (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Select Infinium Kit (Infinium HTS Assay Manual v1.2)

• Master Step Name = Select Infinium Kit-Infinium HTS v1.2

• Step Type = No Outputs

Automations

Set Infinium HTS Kit Name

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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 'input.::Infinium Kit Name:: = step.::Infinium HTS Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Infinium HTS Kits	Text Dropdown	Custom Entries	Presets Infinium Global Screening Array-24 Kit Infinium Asian Screening Array-24 v1.0 BeadChip Infinium iSelect HTS Infinium CoreExome-24 Kit Infinium OmniExpress-24 Kit Infinium Exome-24 Kit Infinium Core-24 Kit Infinium ImmunoArray-24 v2 BeadChip Kit Infinium PsychArray-24 Kit Infinium QC Array-24 Kit Infinium OncoArray-500K BeadChip GGP Porcine Arrays GGP Bovine & Bos Indicus Arrays BovineSNP50 v3 DNA Analysis BeadChip Infinium ShrimpLD-24 BeadChip PorcineSNP60 DNA Analysis Kit v2 MaizeLD BeadChip Kit

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 2: Quantify DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Quantify DNA-Infinium PicoGreen v1.2

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • 1X TE

  • Lambda DNA

  • PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

• 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 true -h false -exp 'step.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	Well	Built-in
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Column

• Destination Containers

  • 96 well plate

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  1X TE (mL)	Numeric	Read Only
  1X TE for A1 (uL)	Numeric	Read Only
  Lambda serial dilution instruction notes	Multiline Text	Read Only	Default = Add 66.7 uL 1X TE to well B1. Add 100 µl 1X TE to the remaining wells of column 1. Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix. Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix. Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
  No. of QDNA Plates	Numeric Dropdown		Presets 1 2 3 Default = 1
  PicoGreen (uL)	Numeric	Read Only
  Sample QDNA Plate instruction notes	Multiline Text	Read Only	Default = Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate. Add 2 µl DNA sample to each well containing PicoGreen/1xTE
  Standard QDNA Plate instruction notes	Multiline Text	Read Only	Default = Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate. Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
  Stock Lambda DNA (ng/uL)	Numeric
  Stock Lambda DNA for A1 (uL)	Numeric	Read Only

• Step File Placeholders

  • Log - Automatically attached

  • Results File - Manually uploaded

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • File Column Options

    • File Column Display = Show

    • File Attachment Method = Manual

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Amplify DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Amplify DNA-Infinium HTS v1.2

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • MA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • MA2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • MSM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • NaOH

Automations

Validate MSA3 Plate Barcode and Set Sample Placement Information

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

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 -exp 'if (!output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {fail ( ::Invalid MSA3 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

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 'output.::Infinium Kit Name:: = input.::Infinium Kit Name::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • 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)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Add 20 µl MA1 to each well of the MSA3 plate. Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate Add 4 µl 0.1N NaOH in to each sample well of the plate Add 34 μl MA2 in to each sample well of the plate. Add 38 μl MSM in to each sample well of the plate Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: Incubate DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Incubate DNA-Infinium v1.2

• Step Type = No Outputs

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Step 5: Fragment DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Fragment DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • FMS-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes (HTS, XT)	Multiline Text	Read Only	Default = Add 25 μl FMS to each well of the plate.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Step 6: Precipitate DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Precipitate DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • 100% 2-propanol

  • PM1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  100% 2-propanol Prep Date	Date
  Blue Pellet Presence	Toggle Switch		Default = None Set
  Comment	Multiline Text
  Instruction Notes (HTS, XT)	Multiline Text	Read Only	Default = Add 50 μl PM1 to each well of the plate Add 155 μl 100% 2-propanol to each sample well

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Step 7: Resuspend DNA (Infinium HTS Assay Manual v1.2)

• Master Step Name = Resuspend DNA-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • RA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes (HTS)	Multiline Text	Read Only	Default = Add 23 µl RA1 to each well of the plate.

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Column

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Protocol 2: BeadChip Processing (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to HTS BeadChip (Infinium HTS Assay Manual v1.2)

• Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • PB2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Generate Sample Placement for Infinium BeadChip

• Trigger Location = Placement

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/infinium/placementpatterns"

Validate BeadChip Barcode

• Trigger Location = Placement

• Trigger Style = Automatic upon exit

/usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

Copy Sample Information

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

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 'output.::Infinium Kit Name:: = input.::Infinium Kit Name:: ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode:: ; output.::Sample_Plate:: = input.::Sample_Plate:: ; output.::Sample_Well:: = input.::Sample_Well:: ; output.::BeadChip Barcode:: = output.container.name ; output.::BeadChip Position:: = output.well' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 24x1 HTS BeadChip Multichannel

  

  • 24x1 HTS BeadChip

  

  • 24x1 HD BeadChip

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  HTS Instruction Notes	Multiline Text	Read Only	Default = Transfer 14 µl each sample from the plate to the appropriate section of the BeadChip

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Step 2: Wash BeadChip (Infinium HTS Assay Manual v1.2)

• Master Step Name = Wash BeadChip-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • PB1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes	Multiline Text	Read Only	Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2

• Step File Placeholders

  • Log - Automatically attached

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	BeadChip Barcode	Text	Read Only
    Derived Sample	BeadChip Position	Text	Read Only
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in

Step 3: Extend and Stain BeadChip (Infinium HTS Assay Manual v1.2)

• Master Step Name = Extend and Stain BeadChip-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • ATM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • EDTA

  • EML-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • LX1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • LX2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • PB1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • RA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • SML-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC3-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC4-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Set Array Instrument

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

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 -exp 'input.::Array Instrument:: = ::iScan::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Automatic upon exit

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}"

Routing Script - iScan

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Array Instrument' \
--FIELD_VALUE 'iScan' \
--WORKFLOW 'iScan v1.0' \
--STEP 'Image Infinium BeadChip (iScan v1.0)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ️ The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

• Sample Table (Column Headers)

  Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
  Container	Container Name	Built-in
  Container	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample Name	Built-in
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  70% EthOH Prep Date	Date
  Comment	Multiline Text
  EDTA Prep Date	Date
  Wash and Coat Beadships 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

• Sample Table

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Array Instrument	Text		Default = iScan
    Derived Sample	BeadChip Barcode	Text	Read Only
    Derived Sample	BeadChip Position	Text	Read Only
    Derived Sample	DNA Plate Barcode	Text	Read Only
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample_Plate	Text
    Derived Sample	Sample_Well	Text
    Project	Project Name	Built-in