The TruSeq DNA Exome v2.0 includes the following functionality:
Preconfigured TruSeq DNA Exome v2.0 protocol that supports the preparation of 96 indexed, paired-end libraries, followed by enrichment using reagents provided in an Illumina® TruSeq® Exome Kit.
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 to any Illumina sequencing instrument.
Protocol 1: Library Prep (TruSeq DNA Exome v2.0)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Normalize DNA (TruSeq DNA Exome v2.0)
Master Step Name = Normalize DNA (TruSeq DNA Exome v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of Normalize DNA master step name may be different depending on the version of IPP installed.
Automations
Calculate Sample Volume & Shearing Buffer Mix
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Fragment DNA (TruSeq DNA Exome v2.0)
Master Step Name = Fragment DNA (TruSeq Exome v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Clean Up Fragmented DNA (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 4: Repair Ends and Select Library Size (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 5: Ligate Adapters (TruSeq DNA Exome v2.0)
Master Step Name = Ligate Adapters (TruSeq DNA Exome v2.0.10)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Add Labels
Label Groups
IDT-ILMN TruSeq DNA-RNA UD 24 Indexes
IDT-ILMN TruSeq DNA-RNA UD 24 Indexes Plate
Record Details
Step Data (Master Step Fields)
Step 6: Enrich DNA Fragments (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 7: Qubit DNA QC (TruSeq DNA Exome v2.0)
Master Step Name = Qubit DNA QC (TruSeq Exome v1.0)
Step Type = Standard QC
Measurement Generation = Fixed, 2
Automations
Average Concentration & Assign QC flags
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
Record Details
Step Data (Master Step Fields)
Step 8: Bioanalyzer QC (TruSeq DNA Exome v2.0)
Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
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
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
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Group of Defaults
Nextera DNA Flex Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Nextera Mate Pair Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Nextera XT DNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
NRCC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq ChIP-Seq Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Methyl Capture EPIC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Rapid Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Access Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Small RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded mRNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded Total RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Targeted RNA Expression Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSight Myeloid Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSight RNA Fusion Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TSCA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Step Data
Group of Defaults = TruSeq Exome Library Validation
Master Step Fields
Step 9: Hybridize Probes (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Record Details
Step Data (Master Step Fields)
Step 10: Capture Hybridize Probes (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 11: Perform Second Hybridization (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Record Details
Step Data (Master Step Fields)
Step 12: Perform Second Capture (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 13: Clean Up Captured Library (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Record Details
Step Data (Master Step Fields)
Step 14: Amplify Enriched Library (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Record Details
Step Data (Master Step Fields)
Step 15: Clean Up Amplified Enriched Library (TruSeq DNA Exome v2.0)
Master Step Name = TruSeq DNA Exome v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of TruSeq DNA Exome 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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 16: Bioanalyzer QC (TruSeq DNA Exome v2.0)
Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
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 and assign QC flags
Trigger Location = Not Used
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Group of Defaults
Nextera DNA Flex Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Nextera Mate Pair Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Nextera XT DNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
NRCC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq ChIP-Seq Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Methyl Capture EPIC Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Rapid Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Access Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq RNA Exome Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Small RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded mRNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Stranded Total RNA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSeq Targeted RNA Expression Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSight Myeloid Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TruSight RNA Fusion Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
TSCA Library Validation
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Step Data
Group of Defaults = TruSeq Exome Library Validation
Master Step Fields
Step 17: Normalize Libraries (TruSeq DNA Exome v2.0)
Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1
The version of Normalize 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
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Reagent Kits
TruSeq Exome Kit
Supplier = Illumina
Catalog Number = 24 - 20020614; 96 - 20020615
Website =
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Placement Pattern = Column
Destination Containers
96 well plate
Default = 10
Notes
Multiline Text
Read Only
Default = DNA Amout (ng) and Total Volume (uL) are both per sample.
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 = Column
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName}
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.
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Decimal Places Displayed = 2
Target Normalization (nM)
Numeric
Required Field
Default = 2
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
ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.
