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TruSeq RNA Access v2.0

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Last updated 16 days ago

Overview

The TruSeq RNA Access v2.0 workflow includes the following functionality:

Preconfigured TruSeq RNA Access v2.0 protocol that supports the conversion of total RNA or FFPE samples into a library of template molecules suitable for subsequent cluster generation and sequencing.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the workflow.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated generation of Bioanalyzer input file that the user may upload to the Bioanalyzer instrument’s Expert Software and use to set up a run.
Automated parsing of a Bioanalyzer instrument's XML result file into the LIMS, and storing of QC measurement records for the completed run.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: TruSeq RNA Access v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Sort Samples (TruSeq RNA Access v2.0)

Master Step Name = Sort Samples (TruSeq RNA Access v2.0.10)
Step Type = No Outputs

The version of Sort Samples master step name 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
- 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
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
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 2: Fragment RNA (TruSeq RNA Access v2.0)

Master Step Name = Fragment RNA v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq RNA Access - 12 Index Set A or B, Box 2
  - Supplier = Illumina
  - Catalog Number = Set A Part # 15052311; Set B Part # 15052312
  - Website = https://support.illumina.com/

Automations

Dilute Total RNA

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.::Sample Volume (ul):: = (step.::Desired Diluted Concentration (ng/uL):: * 8.5) / input.::Concentration:: ; output.::Buffer Volume (ul):: = 8.5 - output.::Sample Volume (ul):: ; output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' -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
  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

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
Thermal Cycler Program
Text
Default = Elution 2 - Frag - Prime
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