# 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 | | 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 | | | No. of QDNA Plates | Numeric Dropdown | | | | PicoGreen (uL) | Numeric | Read Only | | | Sample QDNA Plate instruction notes | Multiline Text | Read Only | | | Standard QDNA Plate instruction notes | Multiline Text | Read Only | | | 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 = #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 = #### Automations
Set DNA Plate Barcode * Trigger Location = Placement * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Copy Infinium Kit Name * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * MSM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * NaOH * RPM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Validate MSA4 Plate Barcode and Set Sample Placement Information * Trigger Location = Placement * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Copy Infinium Kit Name * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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 {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * XC4-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Generate Sample Placement for Infinium BeadChip * Trigger Location = Placement * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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" ``` {% endcode %}
Validate BeadChip Barcode * Trigger Location = Placement * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup /usr/bin/python3 /opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI} ``` {% endcode %}
Copy Sample Information * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) #### Automations
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
#### 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](https://www.illumina.com) * EDTA * PB1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * RA1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * STM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * TEM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * XC1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * XC2-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * XC3-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) * XC4-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://www.illumina.com) #### Automations
Set Array Instrument * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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}" ``` {% endcode %}
Routing Script - iScan * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup 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'" ``` {% endcode %} > ℹ 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 | | | --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/clarity-lims/ilass-and-infinium-arrays/infinium-arrays/infinium-hd-v1.2.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.