Illumina DNA Prep with Enrichment (S) Tagmentation v1.2

Protocol 1: Prep Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Sort Sample (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = No Outputs

Automations

Sort & Set Next Step

• 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 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	NFE Sample Type	Text Dropdown	Required Field	Presets Blood Saliva gDNA FFPE DNA
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 2: Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Blood Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Agencourt AMPure XP beads, 5 ml

    • Supplier = Beckman Coulter
    • Catalog Number = A63880
    • Website = www.beckman.com
  • Flex Lysis Reagent Kit

    • Supplier = Illumina
    • Catalog Number = 20015884
    • Website = www.illumina.com

Automations

Calculate Total Samples & 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 NFE - Blood

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

ℹ The version of the workflow and step for the routing 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% EtOH Prep Date	Date
  BLB (uL)	Numeric		Decimal Places Displayed = 2
  PK1 (uL)	Numeric		Decimal Places Displayed = 2
  Thermal Cycler Program	Text		Default = BLP
  Total Samples	Numeric		Default = 0
  Water (uL)	Numeric		Decimal Places Displayed = 2

• 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	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Saliva Lysis (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Agencourt AMPure XP, 5 ml

    • Supplier = Beckman Coulter
    • Catalog Number = A63880

Automations

Copy NFE Sample Type and Set UDFs

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

Set Next Step - Remove

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

Route NFE - Saliva

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

ℹ The version of the workflow and step for the routing 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% EtOH Prep Date	Date

• 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	80% EtOH (uL)	Numeric
    Derived Sample	NFE Sample Type	Text Dropdown	Required Field	Presets Blood Saliva gDNA FFPE DNA
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Water for Resuspension (uL)	Numeric		Default = 30
    Project	Project Name	Built-in

Step 4: Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Qubit gDNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Assign QC flags

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

Set Next Step and Copy Concentration

• 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
  Criteria 1 - Operator	Text		Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration
  Criteria 1 - Threshold Value	Numeric
  Criteria 2 - Operator	Text		Default = <=
  Criteria 2 - Source Data Field	Text		Default = Concentration
  Criteria 2 - Threshold Value	Numeric

• Step File Placeholders

  • Log - Automatically attached
  • QC Log File - Automatically attached
  • QC Result File - Automatically attached
  • Upload File - Manually uploaded
• 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	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Text	Required Field
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Project	Project Name	Built-in

Step 5: Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Dilute gDNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Copy Concentration

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

Calculate Dilution Volume & Sample Volume

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

Set Next Step - Remove & Copy NFE Sample Type

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

Route NFE - gDNA

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

ℹ The version of the workflow and step for the routing 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
  Desired gDNA Concentration (ng/uL)	Numeric		Decimal Places Displayed = 2
  Dilution Buffer	Text Dropdown	Custom Entries	Presets RSB 10 mM Tris-HCI, pH 7.5–8.5
  Total Volume (uL)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log - Automatically attached
• Sample Table

  • 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	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Text	Required Field
    Derived Sample	Dilution Volume (uL)	Numeric
    Derived Sample	Final Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (uL)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 6: Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Qubit FFPE DNA QC (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Assign QC flags

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

Set Next Step and Copy Concentration

• 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
  Criteria 1 - Operator	Text		Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration
  Criteria 1 - Threshold Value	Numeric
  Criteria 2 - Operator	Text		Default = <=
  Criteria 2 - Source Data Field	Text		Default = Concentration
  Criteria 2 - Threshold Value	Numeric

• Step File Placeholders

  • Log - Automatically attached
  • QC Log File - Automatically attached
  • QC Result File - Automatically attached
  • Upload File - Manually uploaded
• 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	Concentration	Numeric	Required Field	Decimal Places Displayed = 2
    Derived Sample	Conc. Units	Text	Required Field
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Project	Project Name	Built-in

Step 7: Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)

• Master Step Name = Dilute FFPE DNA (Illumina DNA Prep with Enrichment (S) Tagmentation v1.2)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

Automations

Copy Concentration

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

Calculate Dilution Volume & Sample Volume

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

Set Next Step - Advance & Copy NFE Sample Type

• 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