Nextera Rapid Capture Custom Enrichment v2.0

Protocol 1: Nextera Rapid Capture Custom Enrichment v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (NRCC v2.0)

• Master Step Name = Tagment v2.0
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • Nextera Rapid Capture Custom Enrichment Kit, Box 1

    • Supplier = Illumina
    • Catalog Number = FC-140-1007; FC-140-1008; FC-140-1009
    • Website = https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-custom-kit.html
  • Nextera Rapid Capture Custom Enrichment Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-140-1007; FC-140-1008; FC-140-1009
    • Website = https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-custom-kit.html

Automations

Normalize gDNA

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

Set Next Step - Advance

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

Normalize gDNA (Nextera XT)

• 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

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

• 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 2: Clean Up Tagmented DNA (NRCC v2.0)

• Master Step Name = Clean Up v2.0
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}
• Reagent Kits

  • Nextera Rapid Capture Custom Enrichment Kit, Box 1

    • Supplier = Illumina
    • Catalog Number = FC-140-1007; FC-140-1008; FC-140-1009
    • Website = https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-custom-kit.html
  • Nextera Rapid Capture Custom Enrichment Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-140-1007; FC-140-1008; FC-140-1009
    • Website = https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-custom-kit.html

Automations

Set Next Step - Advance

• 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

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  80% EtOH Prep Date	Date

• 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 3: Bioanalyzer QC (DNA) (NRCC v2.0)

• Master Step Name = Bioanalyzer QC (DNA) 5.1.2
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName} Bioanalyzer

The version of Bioanalyzer QC (DNA) master step name may be different depending on the version of IPP installed.

Automations

Generate Bioanalyzer driver file

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

Parse Bioanalyzer XML and assign QC flags

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

Set Next Step - Advance

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

Set Next Step - Output PASS/FAIL

• Trigger Location = Not Used

Set Next Step and Copy to Input

• 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

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Row
  • Placement Pattern = Column
• Destination Containers

  • BioAnalyzer DNA High Sensitivity Chip

  

  • BioAnalyzer DNA 1000 Chip

  

Record Details

Group of Defaults

NRCC

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Peak 2 Size - bp
• Criteria 1 - Threshold Value = 150.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Peak 2 Size - bp
• Criteria 2 - Threshold Value = 1,000.00
• Use strict matching for Bioanalyzer results = No

Peak 2 Size Thresholds

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Peak 2 Size - bp
• Criteria 1 - Threshold Value = 100.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Peak 2 Size - bp
• Criteria 2 - Threshold Value = 1,000.00
• Use strict matching for Bioanalyzer results = No

TruSeq ChIP-Seq

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Region 1 Molarity
• Criteria 1 - Threshold Value = 5.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Region 1 Molarity
• Criteria 2 - Threshold Value = 10.00
• Use strict matching for Bioanalyzer results = No

TruSeq Methyl Capture EPIC

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Peak 2 Size - bp
• Criteria 1 - Threshold Value = 100.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Peak 2 Size - bp
• Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Peak 2 Size - bp
• Criteria 1 - Threshold Value = 150.00
• Criteria 2 - Operator = <=
• Criteria 2 - Source Data Field = Peak 2 Size - bp
• Criteria 2 - Threshold Value = 1,000.00
• Use strict matching for Bioanalyzer results = No

• Step Data

  • Group of Defaults = NRCC
  • 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 Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Use strict matching for Bioanalyzer results	Toggle Switch		Default = None Set

• Step File Placeholders

  • Bioanalyzer Driver File - Automatically attached
  • Bioanalyzer Driver File Generation Log File - Automatically attached
  • Bioanalyzer XML Result File (required) - Manually uploaded
  • Result File (optional) - Manually uploaded
  • PDF Summary File (optional) - Manually uploaded
  • Bioanalyzer XML Parsing Log File - Automatically attached
  • 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	Sample Name	Built-in
    Measurement	A260/280 ratio	Numeric		Decimal Places Displayed = 2
    Measurement	BA Sample Name	Text
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Measurement	Number of Peaks found	Numeric		Decimal Places Displayed = 0
    Measurement	Number of Regions found	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Size - bp	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Sample Comment	Text
    Project	Project Name	Built-in

Step 4: Amplify Tagmented DNA (NRCC v2.0)

• Master Step Name = Amplify Tagmented DNA v2.0
• Step Type = Add Labels
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • Nextera Rapid Capture Custom Enrichment Kit, Box 2

    • Supplier = Illumina
    • Catalog Number = FC-140-1007; FC-140-1008; FC-140-1009
    • Website = https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-custom-kit.html

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

Add Labels

• Label Groups

  • Nextera Rapid Capture Custom Enrichment (NRCC)

Record Details

• Step Data (Master Step Fields)