# Infinium XT Assay Manual v1.2 ## Overview The Infinium XT Assay Manual workflow includes the following functionality. * Preconfigured protocols to prepare 96 DNA samples for use with the 24x4 BeadChip. * Support for custom content for XT format. * 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 XT Assay Manual v1.2) Protocol Type = Sample Prep **Next Steps Configuration**
### Step 1: Amplify DNA (Infinium XT Assay Manual v1.2) * Master Step Name = Amplify DNA-Infinium XT v1.2 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * MA1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * MA2-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * NaOH * RAM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) #### Automations
Validate MSA7 Plate Barcode and Set Sample 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}-MSA7:: ) ) {fail ( ::Invalid MSA7 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA7:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Infinium XT Kit Name and 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 'output.::Infinium Kit Name:: = step.::Infinium XT Kits:: ; 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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Column * Placement Pattern = Column * Destination Containers * 96 well plate #### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------- | -------------- | -------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | Infinium XT Kits | Text | | Default = Infinium XT iSelect-96 Kit | | Instruction Notes | Multiline Text | |

Default =
Add 20 µl MA1 to each well of the plate.
Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate.
Add 4 µl 0.1N NaOH in to each sample well of the plate.
Add 35 μl MA2 in to each sample well of the plate.
Add 35 μl RAM 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 | | | | Project | Project Name | Built-in | | | ### Step 2: Incubate DNA (Infinium XT 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** | | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- | | 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 3: Fragment DNA (Infinium XT 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://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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 (HTS, XT) | Multiline Text | Read Only | Default = Add 25 μl FMS to each well of the plate. | * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- | | 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 4: Precipitate DNA (Infinium XT 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://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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 (HTS, XT) | Multiline Text | Read Only |

Default =
Add 50 μl PM1 to each well of the plate
Add 155 μl 100% 2-propanol to each sample well

| * Step File Placeholders * Log - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Column * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- | | 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 5: Resuspend DNA (Infinium XT 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://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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 | | | * 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 XT Assay Manual v1.2) Protocol Type = Sample Prep **Next Steps Configuration**
### Step 1: Hybridize DNA to XT BeadChip (Infinium XT Assay Manual v1.2) * Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * PB2-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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 * 24x4 XT BeadChip
#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | XT Instruction Notes | Multiline Text | Read Only |

Default = Using a 20 μl, 8-channel precision pipette, dispense 15 μl DNA sample into the appropriate BeadChip
sections.

| * 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 XT 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://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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** | | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- | | 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 | | | ### Step 3: Extend and Stain BeadChip (Infinium XT Assay Manual v1.2) * Master Step Name = Extend and Stain BeadChip-Infinium v1.2 * Step Type = No Outputs * Reagent Kits * 70% EtOH * ATM-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * EDTA * EML-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * LX1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * LX2-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * PB1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * RA1-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * SML-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com) * XC3-Infinium * Supplier = Illumina * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/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 | 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.
225 µl LX1. Incubate for 10 minutes.Repeat once.
225 µl LX2. Incubate for 10 minutes. Repeat once.
300 µl EML. Incubate for 15 minutes.
250 µl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat twice.Incubate 5 minutes.
Set the the chamber rack temperature to the temperature indicated on the SML tube.
250 µl XC3. Incubate for 1 minute. Repeat twice.

| | Stain Instruction Notes | Multiline Text | Read Only |

Default =
Fill the reservoir of each flow-through chamber as follows:
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes. g 250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
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.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/infinium-xt-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.