Infinium HD Methylation Assay Manual v1.2

Overview

The Infinium HD Methylation Assay Manual workflow includes the following functionality.

• Preconfigured protocols to prepare 96 DNA samples for use with the 8x1 HD BeadChip products.

• Automated calculation of sample and buffer volumes.

• 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 HD Methylation Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

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

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

• Step Type = No Outputs

Automations

Set Infinium HD Methylation 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 HD Methylation 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
  Container	Container Name	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
  Infinium HD Methylation Kits	Text	Required Field Read Only	Default = Infinium MethylationEPIC 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
    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 2: Quantify DNA (Infinium HD Methylation 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
  Derived Sample	Infinium Kit Name	Text	Read Only

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• 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
    Derived Sample	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in

Step 3: Bisulfite Conversion (Infinium HD Methylation Assay Manual v1.2)

• Master Step Name = Bisulfite Conversion-Infinium v1.2

• Step Type = No Outputs

• Reagent Kits

  • EZ DNA Methylation Kit

    • Supplier = Zymo Research

    • Website = https://www.zymoresearch.com/collections/ez-dna-methylation-kits

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	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
  Cleanup Conversion Reagent Instruction Notes	Multiline Text	Read Only	Default = Use the instructions in the Zymo EZ DNA Methylation Kit to do the following. Clean the samples using the provided spin columns or filter plate. Wash off the remaining conversion reagent. Centrifuge the plate at 3000–5000 × g. Desulphonate the column or the plate with desulphonation buffer. Incubate at room temperature for 15 minutes. Clean the samples and wash to remove the desulphonation buffer. Repeat one time. Add 12 µl elution buffer from 500 ng gDNA. Centrifuge to elute at 3000–5000 × g for 5 minutes
  Denature DNA instruction Notes	Multiline Text	Read Only	Default = Follow the instructions in the Zymo EZ DNA Methylation Kit to denature the genomic DNA and add conversion reagent.
  Incubate DNA Instruction Notes	Multiline Text	Read Only	Default = Incubate in a thermal cycler using the following settings for 16 cycles: 95°C for 30 seconds 50°C for 1 hour Hold DNA at 4°C for 10 minutes in the thermal cycler until cleanup

• 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	Infinium Kit Name	Text	Read Only
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: Create BCD Plate (Infinium HD Methylation Assay Manual v1.2)

• Master Step Name = Create BCD Plate-Infinium v1.2

• Step Type = Standard

• Reagent Kits

  • EZ DNA Methylation Kit

    • Supplier = Zymo Research

    • Website = https://www.zymoresearch.com/collections/ez-dna-methylation-kits

Automations

Set DNA Plate Barcode

• 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 '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

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Instruction Notes	Multiline Text	Read Only	Default = Apply a BCD barcode label Transfer the BCD to the plate as follows: Midi plate: 20 µl BCD sample to each well (requires ≥ 1000 ng input in bisulfite conversion) TCY plate: 10 µl BCD sample to each well (requires ≥ 500 ng input in bisulfite conversion

• 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	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 5: Amplify DNA (Infinium HD Methylation Assay Manual v1.2)

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

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • MA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • MSM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • NaOH

  • RPM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

Automations

Validate MSA4 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}-MSA4:: ) ) {fail ( ::Invalid MSA4 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA4:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.::DNA Plate Barcode::}' -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	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 = 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 plate Transfer 4 µl DNA sample from the BCD plate to the corresponding wells of the plate Add 4 µl 0.1N NaOH in to each sample well of the plate Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g Add 68 μl RPM in to each sample well of the plate Add 75 μl MSM in to each sample well of the plate

• 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	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: Incubate DNA (Infinium HD Methylation 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 7: Fragment DNA (Infinium HD Methylation 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 = 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 (HD Methylation & LCG)	Multiline Text	Read Only	Default = Add 50 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
    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

Step 8: Precipitate DNA (Infinium HD Methylation 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/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
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

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 (HD Methylation & LCG)	Multiline Text	Read Only	Default = Add 100 μl PM1 to each well of the plate. Add 300 μl 100% 2-propanol 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
    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

Step 9: Resuspend DNA (Infinium HD Methylation 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
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Instruction Notes (HD Methylation & LCG)	Multiline Text	Read Only	Default = Add 46 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
    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

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

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize DNA to HD BeadChip (Infinium HD Methylation 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

  • 70% EtOH

  • PB2-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC4-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
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

  • Placement Pattern = Row

• Destination Containers

  • 8x1 HD BeadChip

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  HD Methylation Instruction Notes	Multiline Text	Read Only	Default = Transfer 26 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
    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

Step 2: Wash BeadChip (Infinium HD Methylation 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
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text

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 HD Methylation 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

  • PB1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • RA1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • STM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • TEM-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC1-Infinium

    • Supplier = Illumina

    • Website = www.illumina.com

  • XC2-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
  Derived Sample	DNA Plate Barcode	Text	Read Only
  Derived Sample	Infinium Kit Name	Text	Read Only
  Derived Sample	Sample_Plate	Text
  Derived Sample	Sample_Well	Text

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Extend Instruction Notes (HD Methylation)	Multiline Text	Read Only	Default = Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows: 150 µl RA1. Incubate for 30 seconds. Repeat 5 times. 450 μl XC1. Incubate for 10 minutes. 450 μl XC2. Incubate for 10 minutes. 200 μl TEM. Incubate for 15 minutes. 450 μl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat once. Incubate 5 minutes. Begin ramping the Chamber Rack temperature to the temperature indicated on the STM tube, or to 37°C if none is shown 450 μl XC3. Incubate for 1 minute. Repeat once.
  Stain Instruction Notes (HD Methylation)	Multiline Text		Default = Fill the reservoir of each flow-through chamber as follows: 250 μl STM. Incubate for 10 minutes. 450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes. 250 µl ATM. Incubate for 10 minutes. 450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes. 250 μl STM and incubate for 10 minutes. 450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes. 250 µl ATM. Incubate for 10 minutes. 450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes. 250 μl STM. Incubate for 10 minutes. 450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
  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
    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