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
- MA2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH
- RAM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Validate MSA7 Plate Barcode and Set Sample 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}-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}"

Set Infinium XT Kit Name and 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 'output.::Infinium Kit Name:: = step.::Infinium XT Kits:: ; nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = 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
Required Field
Read Only
Default = Infinium XT iSelect-96 Kit
Instruction Notes
Multiline Text
Read Only
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

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
  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

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 (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

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 (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

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
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

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
- 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

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
  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
- EDTA
- EML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- LX2-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- PB1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- RA1-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- SML-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- XC3-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com

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'"

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

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