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Infinium HTS Assay Manual v1.2

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Last updated 16 days ago

Overview

The Infinium HTS Assay Manual workflow includes the following functionality.

Preconfigured Infinium HTS Assay Manual protocols.
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 HTS Assay Manual v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

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

Master Step Name = Select Infinium Kit-Infinium HTS v1.2
Step Type = No Outputs

Automations

Set Infinium HTS 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 HTS Kits::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
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 HTS Kits
Text Dropdown
Custom Entries
Presets
Infinium Global Screening Array-24 Kit
Infinium Asian Screening Array-24 v1.0 BeadChip
Infinium iSelect HTS
Infinium CoreExome-24 Kit
Infinium OmniExpress-24 Kit
Infinium Exome-24 Kit
Infinium Core-24 Kit
Infinium ImmunoArray-24 v2 BeadChip Kit
Infinium PsychArray-24 Kit
Infinium QC Array-24 Kit
Infinium OncoArray-500K BeadChip
GGP Porcine Arrays
GGP Bovine & Bos Indicus Arrays
BovineSNP50 v3 DNA Analysis BeadChip
Infinium ShrimpLD-24 BeadChip
PorcineSNP60 DNA Analysis Kit v2
MaizeLD BeadChip 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
  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: Quantify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- 1X TE
- Lambda DNA
- PicoGreen dsDNA quantification reagent

Automations

Calculate Stock Lambda DNA and PicoGreen Dilution

Trigger Location = Record Details
Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'step.::Stock Lambda DNA for A1 (uL):: = (233.3 * 75) / step.::Stock Lambda DNA (ng/uL):: ; step.::1X TE for A1 (uL):: = 233.3 - step.::Stock Lambda DNA for A1 (uL):: ; if (step.::No. of QDNA Plates:: == 1) {step.::PicoGreen (uL):: = 115 ; step.::1X TE (mL):: = 23} ; if (step.::No. of QDNA Plates:: == 2) {step.::PicoGreen (uL):: = 215 ; step.::1X TE (mL):: = 43} ; if (step.::No. of QDNA Plates:: == 3) {step.::PicoGreen (uL):: =  315 ; step.::1X TE (mL):: = 63}' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
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

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
1X TE (mL)
Numeric
Read Only
1X TE for A1 (uL)
Numeric
Read Only
Lambda serial dilution instruction notes
Multiline Text
Read Only
Default = Add 66.7 uL 1X TE to well B1. Add 100 µl 1X TE to the remaining wells of column 1. Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix. Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix. Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
No. of QDNA Plates
Numeric Dropdown
Presets
1
2
3
Default = 1
PicoGreen (uL)
Numeric
Read Only
Sample QDNA Plate instruction notes
Multiline Text
Read Only
Default = Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate. Add 2 µl DNA sample to each well containing PicoGreen/1xTE
Standard QDNA Plate instruction notes
Multiline Text
Read Only
Default = Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate. Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Stock Lambda DNA (ng/uL)
Numeric
Stock Lambda DNA for A1 (uL)
Numeric
Read Only
Step File Placeholders
- Log - Automatically attached
- Results File - Manually uploaded
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Collapse
- Well Sort Order = Row
- File Column Options
  - File Column Display = Show
  - File Attachment Method = Manual
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  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 3: Amplify DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Amplify DNA-Infinium HTS 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
- MSM-Infinium
  - Supplier = Illumina
  - Website = www.illumina.com
- NaOH

Automations

Validate MSA3 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}-MSA3:: ) ) {fail ( ::Invalid MSA3 Plate Barcode. Please verify and try again.:: ) } ; if (output.container.name.matches( ::[A-Z]{2}[0-9]{7}-MSA3:: ) ) {output.::Sample_Plate:: = output.container.name ; output.::Sample_Well:: = output.well ; output.::DNA Plate Barcode:: = input.container.name}' -log {compoundOutputFileLuid0}"

Copy Infinium Kit Name

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Infinium Kit Name:: = input.::Infinium Kit Name::' -log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

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 MSA3 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 34 μl MA2 in to each sample well of the plate. Add 38 μl MSM in to each sample well of the plate Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.
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
  Project
  Project Name
  Built-in

Step 4: Incubate DNA (Infinium HTS Assay Manual v1.2)

Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes
Multiline Text
Read Only
Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  DNA Plate Barcode
  Text
  Read Only
  Derived Sample
  Infinium Kit Name
  Text
  Read Only
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample_Plate
  Text
  Derived Sample
  Sample_Well
  Text
  Project
  Project Name
  Built-in

Step 5: Fragment DNA (Infinium HTS 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