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Nextera

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}

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

Record Details

Step Data (Master Step Fields)

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)

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

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

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}

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

Record Details

Step Data (Master Step Fields)

Step 5: Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Pippin Prep Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 6: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ The version of Agarose Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 7: 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}

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

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 & Copy to Input

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Set Next Step - Output PASS/FAIL

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)

Step 8: Circularize DNA (Nextera Mate Pair v1.0)

Master Step Name = Circularize DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1

ℹ The version of Circularize 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

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

Record Details

Step Data (Master Step Fields)

Step 9: Remove Linear DNA (Nextera Mate Pair v1.0)

Master Step Name = Remove Linear DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1

ℹ The version of Remove Linear DNA 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 10: Shear Circularization DNA (Nextera Mate Pair v1.0)

Master Step Name = Shear Circularization DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

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

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)

Step 11: Purify Sheared DNA (Nextera Mate Pair v1.0)

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

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

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 12: End Repair (Nextera Mate Pair v1.0)

Master Step Name = End Repair (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 2

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

Automations

Master Mix Calculations

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

Record Details

Step Data (Master Step Fields)

Step 13: A-Tailing (Nextera Mate Pair v1.0)

Master Step Name = A-Tailing (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- TruSeq DNA LT Library Prep Kit - Set A Box

ℹ The version of A-Tailing master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

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

Record Details

Step Data (Master Step Fields)

Step 14: Ligate Adapters (Nextera Mate Pair v1.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Ligate Adapters 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

Copy to Output

Trigger Location = Not Used

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column

Add Labels

Label Groups
- Nextera Mate Pair

Record Details

Step Data (Master Step Fields)

Step 15: Amplify Libraries (Nextera Mate Pair v1.0)

Master Step Name = Amplify Libraries (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Amplify Libraries 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

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

Record Details

Step Data (Master Step Fields)

Step 16: Clean Up Libraries (Nextera Mate Pair v1.0)

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

ℹ The version of Clean Up 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

Record Details

Step Data (Master Step Fields)

Step 17: Bioanalyzer QC (Library Validation) (Nextera Mate Pair v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Copy nM 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

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Targeted RNA Expression Library Validation

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

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00

Step Data
- Group of Defaults = Nextera Mate Pair Library Validation
- Master Step Fields

Step 18: Normalize Libraries (Nextera Mate Pair v1.0)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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

Automations

Normalization Calculations - Option 1

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step - Remove

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)

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}

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

Record Details

Step Data (Master Step Fields)

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)

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

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

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}

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

Record Details

Step Data (Master Step Fields)

Step 5: Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Pippin Prep Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Pippin Prep Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 6: Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0)

Master Step Name = Agarose Size Selection - Gel-Plus Only (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

ℹ The version of Agarose Size Selection - Gel-Plus Only master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 7: 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}

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

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 & Copy to Input

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Set Next Step - Output PASS/FAIL

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)

Step 8: Circularize DNA (Nextera Mate Pair v1.0)

Master Step Name = Circularize DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1

ℹ The version of Circularize 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

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

Record Details

Step Data (Master Step Fields)

Step 9: Remove Linear DNA (Nextera Mate Pair v1.0)

Master Step Name = Remove Linear DNA (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 1

ℹ The version of Remove Linear DNA 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 10: Shear Circularization DNA (Nextera Mate Pair v1.0)

Master Step Name = Shear Circularization DNA (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

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

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)

Step 11: Purify Sheared DNA (Nextera Mate Pair v1.0)

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

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

Automations

Set Next Step & Copy 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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 12: End Repair (Nextera Mate Pair v1.0)

Master Step Name = End Repair (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- Nextera Mate Pair Library Prep Kit - Box 2

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

Automations

Master Mix Calculations

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

Record Details

Step Data (Master Step Fields)

Step 13: A-Tailing (Nextera Mate Pair v1.0)

Master Step Name = A-Tailing (Nextera Mate Pair v1.0.10)
Step Type = No Outputs
Reagent Kits
- TruSeq DNA LT Library Prep Kit - Set A Box

ℹ The version of A-Tailing master step name may be different depending on the version of IPP installed.

Automations

Master Mix Calculations

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

Record Details

Step Data (Master Step Fields)

Step 14: Ligate Adapters (Nextera Mate Pair v1.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Ligate Adapters 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

Copy to Output

Trigger Location = Not Used

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column

Add Labels

Label Groups
- Nextera Mate Pair

Record Details

Step Data (Master Step Fields)

Step 15: Amplify Libraries (Nextera Mate Pair v1.0)

Master Step Name = Amplify Libraries (Nextera Mate Pair v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

ℹ The version of Amplify Libraries 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

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

Record Details

Step Data (Master Step Fields)

Step 16: Clean Up Libraries (Nextera Mate Pair v1.0)

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

ℹ The version of Clean Up 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

Record Details

Step Data (Master Step Fields)

Step 17: Bioanalyzer QC (Library Validation) (Nextera Mate Pair v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Copy nM 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

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Targeted RNA Expression Library Validation

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

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00

Step Data
- Group of Defaults = Nextera Mate Pair Library Validation
- Master Step Fields

Step 18: Normalize Libraries (Nextera Mate Pair v1.0)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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

Automations

Normalization Calculations - Option 1

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step - Remove

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)

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}

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)
Step File Placeholders

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}

Automations

Set Next Step - Advance

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column

Record Details

Group of Defaults

NRCC

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Peak 2 Size Thresholds

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

TruSeq ChIP-Seq

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Molarity
Criteria 1 - Threshold Value = 5.00

TruSeq Methyl Capture EPIC

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

TruSeq Rapid Exome

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Step Data
- Group of Defaults = NRCC
- Master Step Fields

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}

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

Add Labels

Label Groups
- Nextera Rapid Capture Custom Enrichment (NRCC)

Record Details

Step Data (Master Step Fields)

Step 5: Clean Up Amplified DNA (NRCC v2.0)

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

Automations

Set Next Step - Advance

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)

Step 6: Bioanalyzer QC (Library Validation) (NRCC v2.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Calculate nM 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

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Copy nM and Assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column

Record Details

Step Data (Master Step Fields)

Step 7: Hybridize Probes (NRCC v2.0)

Master Step Name = Hybridize with Pooling v2.0
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}

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

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Placement = Enabled

Defaults
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers

Record Details

Step Data (Master Step Fields)

Step 8: Capture Hybridized Probes (NRCC v2.0)

Master Step Name = Capture Hybridized Probes v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Calculate Master Mix

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 9: Perform Second Hybridization (NRCC v2.0)

Master Step Name = Perform Second Hybridization v2.0
Step Type = No Outputs
Reagent Kits
- Nextera Rapid Capture Custom Enrichment Kit, Box 2

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

Record Details

Step Data (Master Step Fields)

Step 10: Perform Second Capture (NRCC v2.0)

Master Step Name = Perform Second Capture v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders

Step 11: Clean Up Captured Library (NRCC v2.0)

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

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

Record Details

Step Data (Master Step Fields)

Step 12: Amplify Enriched Library (NRCC v2.0)

Master Step Name = Amplify Enriched Library v2.0
Step Type = No Outputs
Reagent Kits
- Nextera Rapid Capture Custom Enrichment Kit, Box 2

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

Record Details

Step Data (Master Step Fields)

Step 13: Clean Up Amplified Enriched Library (NRCC v2.0)

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

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

Record Details

Step Data (Master Step Fields)

Step 14: Bioanalyzer QC (Library Validation) (NRCC v2.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Copy nM 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

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Targeted RNA Expression Library Validation

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

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00

Step Data
- Group of Defaults = NRCC Library Validation
- Master Step Fields

Step 15: Normalize Libraries (NRCC v2.0)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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

Automations

Normalization Calculations - Option 1

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step - Remove

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

ℹ The field value and 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

Record Details

Step Data (Master Step Fields)

Nextera XT v2.0

Overview

The Nextera XT DNA includes the following functionality:

Preconfigured Nextera XT DNA protocol that converts the mRNA in total RNA into a library of template molecules of known strand origin. The library is suitable for subsequent cluster generation and DNA 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.
A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: Nextera XT DNA v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Nextera XT DNA v2.0)

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

Automations

Normalize gDNA (Nextera XT)

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Normalize gDNA

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row

Record Details

Step Data (Master Step Fields)

Step 2: Amplify Libraries (Nextera XT DNA v2.0)

Master Step Name = Amplification with Labels v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Copy to Output

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Add Labels

Label Groups
- Nextera XT v2 Full Set
- Nextera XT v2 Set A
- Nextera XT v2 Set B

Record Details

Step Data (Master Step Fields)

Step 3: Clean Up Libraries (Nextera XT DNA v2.0)

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

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

Record Details

Step Data (Master Step Fields)

Step 4: Bioanalyzer QC (Library Validation) (Nextera XT DNA v2.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Copy nM 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

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00

TruSeq Targeted RNA Expression Library Validation

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

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00

Step Data
- Group of Defaults = Nextera XT DNA Library Validation Validation
- Master Step Fields

Step 5: Normalize Libraries (Nextera XT DNA v2.0)

Master Step Name = Normalize Libraries 3 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

The version of Normalized Libraries 3 master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - Remove

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

ℹ The field name, workflow version and step version for the Sequencing Instrument may vary depending on the version of the IPP.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table

Record Details

Step Data (Master Step Fields)