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TruSeq RNA Exome v1.0

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Last updated 2 months ago

Overview

TruSeq RNA Exome v1.0 includes the following functionality:

Preconfigured TruSeq RNA Exome v1.0 protocol that explains how to convert total RNA into a library of template molecules of known strand origin, then capture the coding regions of the transcriptome using the reagents provided in Illumina® TruSeq® RNA Access Library Prep kits. The resulting library is 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 protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.

Protocol 1: TruSeq RNA Exome v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment RNA (TruSeq RNA Exome v1.0)

Master Step Name = Fragment RNA v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq RNA Library Prep for Enrichment
  - Supplier = Illumina
  - Catalog Number = 20020189
  - Website = www.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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Desired Diluted Concentration (ng/uL)
Numeric
Required Field
Decimal Places Displayed = 1
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
  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
  Project
  Project Name
  Built-in

Step 2: Synthesize First Strand cDNA (TruSeq RNA Exome v1.0)

Master Step Name = First Strand cDNA Synthesis v2.0
Step Type = No Outputs
Reagent Kits
- SuperScript II Reverse Transcriptase
  - Supplier = Life Technologies
  - Catalog Number = 18064-014
  - Website = http://www.lifetechnologies.com/order/catalog/product/18064014
- TruSeq RNA Library Prep for Enrichment
  - Supplier = Illumina
  - Catalog Number = 20020189
  - Website = www.illumina.com

Automations

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 = Column
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
Thermal Cycler Program
Text Dropdown
Custom Entries
Presets
Synthesize 1st Strand
1stSS
Default = Synthesize 1st Strand
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
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Synthesize Second Strand cDNA (TruSeq RNA Exome v1.0)

Master Step Name = Second Strand cDNA Synthesis v2.0
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
- TruSeq RNA Library Prep for Enrichment
  - Supplier = Illumina
  - Catalog Number = 20020189
  - Website = www.illumina.com