Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1

PreviousIllumina Stranded mRNA Prep Ligation 1.1 NextiLASS

Last updated 1 month ago

Protocol 1: Prep Sample (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Hybridize Probes (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Hybridize Probes for Stranded Total RNA Prep v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Calculate Hybridize Probe Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::DB1 (uL):: = 3.6 * step.::Total Samples:: ; step.::DP1 (uL):: = 1.2 * step.::Total Samples::' \
-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 = Column
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 2: Deplete rRNA (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Deplete rRNA v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Calculate rRNA Depletion Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::RDB (uL):: = 4.8 * step.::Total Samples:: ; step.::RDE (uL):: = 1.2 * step.::Total Samples::' \
-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 = Column
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 3: Remove Probes (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Remove Probes v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Calculate Removal Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::PRB (uL):: = 7.7 * step.::Total Samples:: ; step.::PRE (uL):: = 3.3 * step.::Total Samples::' \
-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 = Column
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 4: Clean Up RNA (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Clean Up RNA v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 5: Fragment and Denature RNA (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Fragment and Denature RNA v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Synthesize First Strand cDNA (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Synthesize First Strand cDNA v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - Website = www.illumina.com

Automations

Calculate First Strand Synthesis Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; step.::FSA (uL):: = 9 * step.::Total Samples:: ; step.::RVT (uL):: = 1 * step.::Total Samples:: ' -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 = Column
Sample Table (Column Headers)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 7: Synthesize Second Strand cDNA (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Synthesize Second Strand cDNA v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Agencourt AMPure XP, 5 ml
  - Supplier = Beckman Coulter
  - Catalog Number = A63880
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Protocol 2: Library Prep (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Adenylate 3ʹ Ends (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Adenylate 3ʹ Ends - RNA Prep v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 2: Ligate Anchors (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Ligate Anchors - RNA Prep v1.0
Step Type = No Outputs
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 3: Clean Up Fragments (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Clean Up Fragments - RNA Prep v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Agencourt AMPure XP, 5 ml
  - Supplier = Beckman Coulter
  - Catalog Number = A63880
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 4: Amplify Library (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Amplify Library - RNA Prep v1.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}-{AppliedReagentLabels}
Reagent Kits
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Add Labels

Label Groups
- IDT for Illumina RNA UD Indexes Set A Ligation
- IDT for Illumina RNA UD Indexes Set A-D Ligation
- IDT for Illumina RNA UD Indexes Set B Ligation
- IDT for Illumina RNA UD Indexes Set C Ligation
- IDT for Illumina RNA UD Indexes Set D Ligation
- Illumina RNA UD Indexes Set A B C D Ligation
- Illumina RNA UD Indexes Set A Ligation
- Illumina RNA UD Indexes Set B Ligation
- Illumina RNA UD Indexes Set C Ligation
- Illumina RNA UD Indexes Set D Ligation

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 5: Clean Up Library (Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1)

Master Step Name = Clean Library v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- Agencourt AMPure XP, 5 ml
  - Supplier = Beckman Coulter
  - Catalog Number = A63880
- Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
  - Supplier = Illumina
  - 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)

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields