TruSeq Custom Amplicon v1.0

Protocol 1: TruSeq Custom Amplicon (TSCA) v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit QC (DNA) (TSCA v1.0)

• Master Step Name = Qubit QC (DNA) v1.0
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName} Qubit

Automations

Assign QC flags (Qubit QC)

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

Set Next Step & Copy Concentration

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

Copy Concentration (ng/uL)

• Trigger Location = Not Used

Qubit Copy Conc

• Trigger Location = Not Used

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	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

Group of Defaults

Concentration Thresholds

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Concentration (ng/ul)
• Criteria 1 - Threshold Value = 10.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Concentration (ng/ul)
• Criteria 2 - Threshold Value = 50.00

TSCA

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Concentration (ng/ul)
• Criteria 1 - Threshold Value = 10.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Concentration (ng/ul)

• Step Data

  • Group of Defaults = TSCA
  • Master Step Fields

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Criteria 1 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 1 - Source Data Field	Text Dropdown		Presets Concentration (ng/ul)
    Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration (ng/ul)
    Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Qubit Result File - Manually uploaded
  • QC Assignment Log File - Automatically attached
  • QC Assignment Report - Automatically attached
• Sample Table

  • Enable QC Flags = Yes
  • Sample Display Default = Expand
  • Well Sort Order = Row
  • File Column Options

    • File Column Display = Hide
    • File Attachment Method = Auto
  • 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 (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: Normalize DNA 1 (TSCA v1.0)

• Master Step Name = Normalize DNA 1 (TSCA v1.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • TruSeq Custom Amplicon Low Input Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-134-2002; FC-134-2001
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

The version of Normalized DNA 1 master step name may be different depending on the version of IPP installed.

Automations

Normalize DNA 1 Calculations

• 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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	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
  Final Volume (ul)	Numeric	Required Field	Default = 10 Decimal Places Displayed = 2
  Target Normalization (ng/ul)	Numeric	Required Field	Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - 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	Buffer Volume (ul)	Numeric		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 3: Qubit QC (DNA) (TSCA v1.0)

• Master Step Name = Qubit QC (DNA) v1.0
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName} Qubit

Automations

Assign QC flags (Qubit QC)

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

Set Next Step & Copy Concentration

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

Copy Concentration (ng/uL)

• Trigger Location = Not Used

Qubit Copy Conc

• Trigger Location = Not Used

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	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Record Details

Group of Defaults

Concentration Thresholds

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Concentration (ng/ul)
• Criteria 1 - Threshold Value = 10.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Concentration (ng/ul)
• Criteria 2 - Threshold Value = 50.00

TSCA

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Concentration (ng/ul)
• Criteria 1 - Threshold Value = 10.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Concentration (ng/ul)

• Step Data

  • Group of Defaults = TSCA
  • Master Step Fields

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Criteria 1 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 1 - Source Data Field	Text Dropdown		Presets Concentration (ng/ul)
    Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration (ng/ul)
    Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Qubit Result File - Manually uploaded
  • QC Assignment Log File - Automatically attached
  • QC Assignment Report - Automatically attached
• Sample Table

  • Enable QC Flags = Yes
  • Sample Display Default = Expand
  • Well Sort Order = Row
  • File Column Options

    • File Column Display = Hide
    • File Attachment Method = Auto
  • 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 (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 4: Normalize DNA 2 (TSCA v1.0)

• Master Step Name = Normalize DNA 2 (TSCA v1.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • TruSeq Custom Amplicon Low Input Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-134-2002; FC-134-2001
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

The version of Normalized DNA 2 master step name may be different depending on the version of IPP installed.

Automations

Normalize DNA 2 Calculations

• 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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	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 Input DNA Amount (ng)	Numeric	Required Field	Decimal Places Displayed = 2
  Final Volume (ul)	Numeric	Required Field	Default = 4 Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - 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	Buffer Volume (ul)	Numeric		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 5: Hybridize Oligo Pool (TSCA v1.0)

• Master Step Name = Hybridize Oligo Pool (TSCA v1.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • TruSeq Custom Amplicon Low Input Kit, Box 1

    • Supplier = Illumina
    • Catalog Number = FC-134-2002; FC-134-2001
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html
  • TruSeq Custom Amplicon Low Input Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-134-2002; FC-134-2001
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

The version of Hybridize Oligo Pool master step name may be different depending on the version of IPP installed.

Automations

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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	LIMS ID (Container)	Built-in
    Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
  • Placement Pattern = Row
• 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
  ELE Volume (ul) to add to ELB	Numeric Dropdown	Required Field	Presets 18 137 Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - 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	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: Remove Unbound Oligos (TSCA v1.0)

• Master Step Name = Remove Unbound Oligos (TSCA v1.0.10)
• Step Type = No Outputs
• Reagent Kits

  • TruSeq Custom Amplicon Low Input Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-134-2002; FC-134-2001
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-custom-amplicon-low-input.html

The version of Remove Unbound Oligos master step name may be different depending on the version of IPP installed.

Automations

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	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in

  • Expanded View Fields

    Category	Field Name	Field Type