Infinium HD Methylation Assay Manual v1.2

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Last updated 1 month ago

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

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)
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

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

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)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

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)

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)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

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 \