Illumina DNA Prep (M) Tagmentation v1.0

Overview

The Illumina DNA Prep (M) Tagmentation workflow includes the following functionality.

• Preset Illumina DNA Prep (M) Tagmentation protocols that support the generation of enriched libraries for dual-indexed, paired-end sequencing.
• Automated calculation of sample and buffer volumes.
• Automated calculation or display of reagents at every step in the protocol.
• Automatic step transition when required.
• Automatic placement of samples when necessary.
• Automated assignment of QC Pass/Fail, based on user-selected threshold values.

Protocol 1: Prep Sample (Illumina DNA Prep (M) Tagmentation v1.0.9)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample Type (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Sort Sample v2.0.8
• Step Type = No Outputs

The version of Sort Sample master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Tagmentation

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

ℹ The version of the nextStep step names may be different depending on the version of IPP installed.

Route Samples - Large Complex Genome

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

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

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • 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	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 2: DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = DNA Quantification (Illumina DNA Prep (M) Tagmentation v1.0.9)
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName}

The version of DNA Quantification master step name may be different depending on the version of IPP installed.

Automations

Calculate DNA Amount & Assign QC

• Trigger Location = Record Details
• Trigger Style = Manual button

Set Next Step - Remove

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Route Samples - Small Genomes

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

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

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Enable QC Flags = Yes
  • Sample Display Default = Expand
  • 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	LIMS ID (Container)	Built-in
    Container	Well	Built-in
    Derived Sample	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Measurement	DNA Amount (ng)	Numeric		Decimal Places Displayed = 0
    Measurement	Prep Sample Type - Tagmentation	Text	Read Only
    Measurement	Sample Volume (ul)	Numeric	Required Field	Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 3: Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Blood Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1

    • Supplier = Illumina
  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Flex Lysis Reagent Kit

    • Supplier = Illumina

The version of Blood Lysis master step name may be different depending on the version of IPP installed.

Automations

Count Samples and Calculate Master Mix

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Remove

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Route Samples - Blood

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

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
  80% Ethanol Prep Date	Date
  BLB (uL)	Numeric		Decimal Places Displayed = 2
  Comment	Multiline Text
  Nuclease-free water (uL)	Numeric		Decimal Places Displayed = 2
  PK1 (uL)	Numeric		Decimal Places Displayed = 2
  Thermal Cycler Program	Text		Default = BLP
  Total Samples	Numeric		Default = 0

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • 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	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Saliva Lysis (Illumina DNA Prep (M) Tagmentation v1.0.9)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1

    • Supplier = Illumina

The version of Saliva Lysis master step name may be different depending on the version of IPP installed.

Automations

Copy Prep Sample Type - Tagmentation

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  80% Ethanol Prep Date	Date
  Comment	Multiline Text

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • 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	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Protocol 2: Library Prep (Illumina DNA Prep (M) Tagmentation v1.0.9)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Tagment Genomic DNA v1.0
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2

    • Supplier = Illumina
  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 3

    • Supplier = Illumina

Automations

Copy Prep Sample Type - Tagmentation, DNA Amount & Set Blood and Saliva Sample Volume

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Calculate DNA Amount for SMALL GENOMES

• Trigger Location = Record Details
• Trigger Style = Manual button

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Desired DNA Amount (ng)	Numeric		Decimal Places Displayed = 1
  Directions	Multiline Text		Default = If Sample Type is Small Genome, please enter a Desired DNA Amount (ng) at the top of the screen & press blue button. If Sample Type is Large Complex Genome please enter Sample Volume (ul).
  Thermal Cycler Program	Text		Default = TAG

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • 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	Nuclease-free water (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: Post Tagmentation Clean Up (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Post Tagmentation Clean Up v1.0
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 1

    • Supplier = Illumina

Automations

Copy Prep Sample Type - Tagmentation & DNA Amount

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Thermal Cycler Program	Text		Default = PTC

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • Sample Display Default = Expand
  • 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	Prep Sample Type - Tagmentation	Text Dropdown	Required Field	Presets Blood Saliva Large Complex Genomes Small Genomes
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Amplify Tagmented DNA (Illumina DNA Prep (M) Tagmentation v1.0.9)

• Master Step Name = Amplify Tagmented DNA v3.0
• Step Type = Add Labels
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Illumina DNA (M) Tagmentation Library Prep Kit 48/96, Box 2

    • Supplier = Illumina

Automations

Set Prep Sample Type - Tagmentation & Set PCR Cycles

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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