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TruSeq DNA Exome v2.0

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Last updated 17 days ago

Overview

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
Naming Convention = {InputItemName}
Reagent Kits
- TruSeq Exome Kit
  - Supplier = Illumina
  - Catalog Number = 24 - 20020614; 96 - 20020615
  - Website = www.illumina.com

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

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t true \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Sample Volume (uL):: = step.::DNA Amount (ng):: / output.::Concentration:: ; \
output.::Shearing Buffer Mix (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
-log {compoundOutputFileLuid0}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

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
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
DNA Amount (ng)
Numeric
Read Only
Default = 100
EDTA (uL)
Numeric
Read Only
Default = 10
Notes
Multiline Text
Read Only
Default = DNA Amout (ng) and Total Volume (uL) are both per sample.
RSB (mL)
Numeric
Read Only
Default = 5
Total Volume (uL)
Numeric
Read Only
Default = 50
Decimal Places Displayed = 0
Step File Placeholders
- Log - 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
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (uL)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Shearing Buffer Mix (uL)
  Numeric
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

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
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Exome Kit