The Equalizer Workflow AmpliSeq for Illumina Immune Response Panel is part of the AmpliSeq for Illumina Immune Response Panel protocols that include the following functionality:
Preconfigured AmpliSeq for Illumina Immune Response Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of total RNA using the AmpliSeq for Illumina workflow.
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.
There is no extraction protocol in this workflow because the samples are already extracted.
Protocol Type = Library Prep
Next Steps Configuration
Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Agencourt AMPure XP Beads
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Step Data (Master Step Fields)
Step File Placeholders
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Group of Defaults
Step Data
Group of Defaults = Equalizer Workflow
Master Step Fields
Master Step Name = Perform Capture and Clean Up (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Master Step Name = Elute Library (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement Pattern = Column
Step Data (Master Step Fields)
Step File Placeholders
Supplier = Thermo
Catalog Number = NC9959336; NC9933872
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
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
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
1X Lib AMP Mix (uL)
Numeric
Decimal Places Displayed = 2
10X Library Amp Primers (uL)
Numeric
Decimal Places Displayed = 2
Thermal Cycler Program
Text Dropdown
Custom Entries
Presets
AMP_7
EQUAL
AMP
Total Samples
Numeric
Default = 0
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Reagent Kits
AmpliSeq Library Equalizer for Illumina
Supplier = Illumina
Website = www.illumina.com
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
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)
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
Destination Containers
96 well plate
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Field Name
Field Type
Options
Additional Options and Dropdown Items
70% EtOH Prep Date
Date
Field Name
Field Type
Options
Field Name
Field Type
Options
Additional Options and Dropdown Items
Thermal Cycler Program
Text
Default = ELUTE
Additional Options and Dropdown Items
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}"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 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /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 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
-log {compoundOutputFileLuid0}"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}"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 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /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 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"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}"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}"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
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
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Project
Project Name
Built-in
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