Nextera Mate Pair v1.0

Protocol 1: Nextera Mate Pair v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Nextera Mate Pair v1.0)

• Master Step Name = Tagment Genomic DNA (Nextera Mate Pair v1.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • Nextera Mate Pair Library Prep Kit - Box 1

    • Supplier = Illumina
    • Catalog Number = FC-132-1001
  • Nextera Mate Pair Library Prep Kit - Box 2

    • Supplier = Illumina
    • Catalog Number = FC-132-1001
  • Zymo Genomic DNA Clean & Concentrator

    • Supplier = Zymo Research
    • Catalog Number = D4010 (25 preps) or D4011 (100 preps)

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

Automations

Master Mix Calculations

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

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
  Mate Pair Tagment Enzyme Per Sample Volume (ul)	Numeric Dropdown	Custom Entries	Presets 4 12 Decimal Places Displayed = 2
  Tagment Buffer Mate Pair Per Sample Volume (ul)	Numeric Dropdown	Custom Entries	Presets 20 80 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	Gel Type	Text Dropdown	Required Field	Presets Gel-Free Gel-Plus
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Water Per Sample (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: Bioanalyzer QC (DNA) (Nextera Mate Pair v1.0)

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

Automations

Generate Bioanalyzer Input 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 - Output PASS/FAIL

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

Set Next Step & 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 = Row
• Destination Containers

  • BioAnalyzer DNA 7500 and DNA 1200 Chip

  

  • BioAnalyzer DNA High Sensitivity Chip

  

Record Details

• Step Data (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 Input File - Automatically attached
  • Bioanalyzer Input File Generation Log - 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 3: Strand Displacement (Nextera Mate Pair v1.0)

• Master Step Name = Strand Displacement (Nextera Mate Pair v1.0.10)
• Step Type = No Outputs
• Reagent Kits

  • Nextera Mate Pair Library Prep Kit - Box 1

    • Supplier = Illumina
    • Catalog Number = FC-132-1001
  • Nextera Mate Pair Library Prep Kit - Box 2

    • Supplier = Illumina
    • Catalog Number = FC-132-1001

ℹ The version of Strand Displacement 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

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 = 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	Gel Type	Text Dropdown	Required Field	Presets Gel-Free Gel-Plus
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 4: Purify the DNA (Nextera Mate Pair v1.0)

• Master Step Name = Purify the DNA (Nextera Mate Pair v1.0.10)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • AMPure XP Beads

    • Supplier = Beckman Coulter Genomics
    • Catalog Number = A63881
    • Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
  • Nextera Mate Pair Library Prep Kit - Box 2

    • Supplier = Illumina
    • Catalog Number = FC-132-1001

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

Automations

Set Next Step based on Gel 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	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
  Next Step	Text Dropdown	Required Field	Presets Gel-Free Gel-Plus Pippin Prep Gel-Plus Agarose Gel
  70% EtOH Prep Date	Date

• Step File Placeholders

  • Log File - Automatically attached
• Sample Table

  • Sample Display Default = Collapse
  • Well Sort Order = Row
  • Table Columns - Global Fields

    Category	Field Name