# Infinium HTS Assay Manual v1.2

## 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**

<figure><img src="/files/VTKbawaLwCzlSUudr8Wf" alt=""><figcaption></figcaption></figure>

### 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

<figure><img src="/files/5aJzlUVSWuCprcF3PtbK" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Infinium HTS Kit Name</summary>

* 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 HTS Kits::' -log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### 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 | <p>Presets</p><ul><li>Infinium Global Screening Array-24 Kit</li><li>Infinium Asian Screening Array-24 v1.0 BeadChip</li><li>Infinium iSelect HTS</li><li>Infinium CoreExome-24 Kit</li><li>Infinium OmniExpress-24 Kit</li><li>Infinium Exome-24 Kit</li><li>Infinium Core-24 Kit</li><li>Infinium ImmunoArray-24 v2 BeadChip Kit</li><li>Infinium PsychArray-24 Kit</li><li>Infinium QC Array-24 Kit</li><li>Infinium OncoArray-500K BeadChip</li><li>GGP Porcine Arrays</li><li>GGP Bovine & Bos Indicus Arrays</li><li>BovineSNP50 v3 DNA Analysis BeadChip</li><li>Infinium ShrimpLD-24 BeadChip</li><li>PorcineSNP60 DNA Analysis Kit v2</li><li>MaizeLD BeadChip Kit</li></ul> |
* 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

<figure><img src="/files/lVUes5MEyjoEWjxSKa3s" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Stock Lambda DNA and PicoGreen Dilution</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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   | <ul><li>Default =<br>Add 66.7 uL 1X TE to well B1.<br>Add 100 µl 1X TE to the remaining wells of column 1.<br>Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.<br>Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.<br>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.</li></ul> |
  | No. of QDNA Plates                       | Numeric Dropdown |             | <ul><li><p>Presets</p><ul><li>1</li><li>2</li><li>3</li></ul></li><li>Default = 1</li></ul>                                                                                                                                                                                                                                                                                                                                                                                 |
  | PicoGreen (uL)                           | Numeric          | Read Only   |                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
  | Sample QDNA Plate instruction notes      | Multiline Text   | Read Only   | <ul><li>Default =<br>Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate.<br>Add 2 µl DNA sample to each well containing PicoGreen/1xTE</li></ul>                                                                                                                                                                                                                                                                                          |
  | Standard QDNA Plate instruction notes    | Multiline Text   | Read Only   | <ul><li>Default =<br>Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.<br>Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.</li></ul>                                                                                                                                                                                                    |
  | 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](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)
  * MSM-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com)
  * NaOH

#### Automations

<figure><img src="/files/hRYHBwDDPYED94hWqcYf" alt=""><figcaption></figcaption></figure>

<details>

<summary>Validate MSA3 Plate Barcode and Set Sample Placement Information</summary>

* 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}-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}"
```

{% endcode %}

</details>

<details>

<summary>Copy Infinium Kit Name</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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   | <p>Default =<br>Add 20 µl MA1 to each well of the MSA3 plate.<br>Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate<br>Add 4 µl 0.1N NaOH in to each sample well of the plate<br>Add 34 μl MA2 in to each sample well of the plate.<br>Add 38 μl MSM in to each sample well of the plate<br>Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.</p> |
* 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

<figure><img src="/files/A8fRinJ3FHRSks9MNsIE" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com)

#### Automations

<figure><img src="/files/Nh7owdmt1AJnoCM1LDzj" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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** |
  | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- |
  | 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 | 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** |
    | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- |
    | 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 6: Precipitate DNA (Infinium HTS 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

<figure><img src="/files/0opGbQvcej2EynY4AssS" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### Queue

* 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** |
  | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- |
  | 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 | Waiting           | Built-in       |             |                                           |
  | Project        | Project Name      | Built-in       |             |                                           |

#### 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** |
  | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | 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       |             |                                           |

#### 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   | <p>Default =<br>Add 50 μl PM1 to each well of the plate<br>Add 155 μl 100% 2-propanol to each sample well</p> |
* 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | 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 7: Resuspend DNA (Infinium HTS 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

<figure><img src="/files/WxptzdH7nNAe6uCKGfvo" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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** |
  | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
  | 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**          | **Field Type** | **Options** | **Additional Options and Dropdown Items**          |
  | ----------------------- | -------------- | ----------- | -------------------------------------------------- |
  | Comment                 | Multiline Text |             |                                                    |
  | Instruction Notes (HTS) | Multiline Text | Read Only   | Default = Add 23 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** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | 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       |             |                                           |

## Protocol 2: BeadChip Processing (Infinium HTS Assay Manual v1.2)

Protocol Type = Sample Prep

**Next Steps Configuration**

<figure><img src="/files/RaKLhz32curN16rWIy5N" alt=""><figcaption></figcaption></figure>

### Step 1: Hybridize DNA to HTS BeadChip (Infinium HTS 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

<figure><img src="/files/7V9BSG89MUh72xpoAe0I" alt=""><figcaption></figcaption></figure>

<details>

<summary>Generate Sample Placement for Infinium BeadChip</summary>

* 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 %}

</details>

<details>

<summary>Validate BeadChip Barcode</summary>

* 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 %}

</details>

<details>

<summary>Copy Sample Information</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Row
* Destination Containers

  * 24x1 HTS BeadChip Multichannel

  <figure><img src="/files/tLZITr6eeqO2yKNFyfJ5" alt=""><figcaption></figcaption></figure>

  * 24x1 HTS BeadChip

  <figure><img src="/files/GAh0012Tz7sbJqXANIqj" alt=""><figcaption></figcaption></figure>

  * 24x1 HD BeadChip

  <figure><img src="/files/TTQghhI9dSTC8qoS4nmg" alt=""><figcaption></figcaption></figure>

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**        | **Field Type** | **Options** | **Additional Options and Dropdown Items**                                                      |
  | --------------------- | -------------- | ----------- | ---------------------------------------------------------------------------------------------- |
  | Comment               | Multiline Text |             |                                                                                                |
  | HTS Instruction Notes | Multiline Text | Read Only   | Default = Transfer 14 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** |
    | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name    | 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 2: Wash BeadChip (Infinium HTS 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

<figure><img src="/files/PLPmeJutTqR6TPyQQk1y" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 | Sample\_Plate       | Text           |             |                                           |
  | Derived Sample | Sample\_Well        | Text           |             |                                           |
  | 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 = 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 HTS 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://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)
  * XC4-Infinium
    * Supplier = Illumina
    * Website = [www.illumina.com](https://help.claritylims.illumina.com/ilass-and-infinium-arrays/infinium-arrays/www.illumina.com)

#### Automations

<figure><img src="/files/7QzeiMGpYVjjTBMOBWSA" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Array Instrument</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

<details>

<summary>Routing Script - iScan</summary>

* 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.

</details>

#### 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 | Sample\_Plate       | Text           |             |                                           |
  | Derived Sample | Sample\_Well        | Text           |             |                                           |
  | 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**                                                       |
  | ----------------------------------------- | -------------- | ----------- | ----------------------------------------------------------------------------------------------- |
  | 70% EthOH Prep Date                       | Date           |             |                                                                                                 |
  | Comment                                   | Multiline Text |             |                                                                                                 |
  | EDTA Prep Date                            | Date           |             |                                                                                                 |
  | Wash and Coat Beadships Instruction Notes | Multiline Text | Read Only   | <p>Default =<br>Add 310 ml PB1 to the PB1 wash dish.<br>Add 310 ml XC4 to the XC4 wash dish</p> |
* 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 | 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           |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |


---

# 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-hts-v1.2.md?ask=<question>
```

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.