TruSeq Small RNA v1.0

Overview

TruSeq Small RNA v1.0 includes the following functionality:

• Preconfigured TruSeq Small RNA v1.0 protocol that explains how to prepare total RNA or purified small RNA using a Illumina® TruSeq® Small RNA Library Prep 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 using any Illumina sequencing instrument.

It is not required to have the total RNA samples quantified prior to starting this protocol, however it is highly recommended to ensure the starting number of samples.

Protocol 1: TruSeq Small RNA v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Ligate Adapters (TruSeq Small RNA v1.0)

• Master Step Name = Ligate Adapters (TruSeq Small RNA v1.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • T4 RNA Ligase 2, Deletion Mutant

    • Supplier = Epicentre

    • Catalog Number = LR2D1132K; LR2D11310K

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

  • TruSeq Small RNA Library Prep Kit, Indices A, B, C or D

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

• Control Types

  • Human Brain Total RNA

    • Supplier = Thermo Fisher Scientific

    • Catalog Number = AM7962

The version of Ligate Adapters master step name may be different depending on the version of IPP installed.

Automations

Calculate 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} -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.::HML Volume (ul):: = step.::Total samples:: * 2.2) ; (step.::RNase Inhibitor Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::T4 RNA Ligase 2, Depletion Mutant Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::RA5 Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::10mM ATP Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::T4 RNA Ligase Volume (ul):: = step.::Total samples:: * 1.21)' -log {compoundOutputFileLuid1}"

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
  HML Volume (ul)	Numeric		Decimal Places Displayed = 2
  RA5 Volume (ul)	Numeric		Decimal Places Displayed = 2
  RNase Inhibitor Volume (ul)	Numeric		Decimal Places Displayed = 2
  T4 RNA Ligase 2, Depletion Mutant Volume (ul)	Numeric		Decimal Places Displayed = 2
  T4 RNA Ligase Volume (ul)	Numeric		Decimal Places Displayed = 2
  10mM ATP Volume (ul)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - Automatically attached

  • 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 2: Perform Reverse Transcription (TruSeq Small RNA v1.0)

• Master Step Name = Perform Reverse Transcription (TruSeq Small RNA v1.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • SuperScript II Reverse Transcriptase

    • Supplier = Life Technologies

    • Catalog Number = 18064-014

    • Website = http://www.lifetechnologies.com/order/catalog/product/18064014

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

  • TruSeq Small RNA Library Prep Kit, Indices A, B, C or D

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

The version of Perform Reverse Transcription master step name may be different depending on the version of IPP installed.

Automations

Calculate 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} -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.::5X First Strand Buffer Volume (ul):: = step.::Total samples:: * 2.2) ; (step.::12.5 mM dNTP Mix Volume (ul):: = step.::Total samples:: * 0.55) ; (step.::100mM DTT Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::RNase Inhibitor Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::SuperScript II Reverse Transcriptase Volume (ul):: = step.::Total samples:: * 1.1)' -log {compoundOutputFileLuid1}"

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
  Dilute 25mM dNTP mix to 12.5mM (per library): 0.5ul of 25mM dNTP Mix and 0.5ul of Ultrapure water.	Toggle Switch		Default = None Set
  RNase Inhibitor Volume (ul)	Numeric		Decimal Places Displayed = 2
  SuperScript II Reverse Transcriptase Volume (ul)	Numeric		Decimal Places Displayed = 2
  5X First Strand Buffer Volume (ul)	Numeric		Decimal Places Displayed = 2
  12.5 mM dNTP Mix Volume (ul)	Numeric		Decimal Places Displayed = 2
  100mM DTT Volume (ul)	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - Automatically attached

  • 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: Amplify Libraries (TruSeq Small RNA v1.0)

• Master Step Name = Amplify Libraries (TruSeq Small RNA v1.0.10)

• Step Type = Add Labels

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

  • TruSeq Small RNA Library Prep Kit, Indices A, B, C or D

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

The version of Amplify Libraries master step name may be different depending on the version of IPP installed.

Automations

Calculate 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} -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.::Ultrapure water Volume (ul):: = step.::Total samples:: * 9.35) ; (step.::PML Volume (ul):: = step.::Total samples:: * 27.5) ; (step.::RP1 Volume (ul):: = (step.::Total samples:: * 2.2).round(2)) ' -log {compoundOutputFileLuid1}"

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 = Enabled

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Column

  • Placement Pattern = Column

• Destination Containers

  • Tube

Add Labels

• Label Groups

  • TruSeq Small RNA

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Ultrapure water Volume (ul)	Numeric		Decimal Places Displayed = 2
  PML Volume (ul)	Numeric		Decimal Places Displayed = 2
  RP1 Volume (ul)	Numeric		Decimal Places Displayed = 2
  Add 2ul of chosen RPIX to each sample.	Toggle Switch		Default = None Set

• Step File Placeholders

  • Log File - Automatically attached

  • Log File - Automatically attached

• 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 4: Bioanalyzer QC (Library Validation) (TruSeq Small RNA v1.0)

• Master Step Name = Bioanalyzer QC (Library Validation) v2.0

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

• 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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}  && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"

Parse Bioanalyzer XML and assign QC flags

• 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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step - Output PASS/FAIL

• 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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML, Calculate nM and assign QC flags

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Parse Bioanalyzer XML, Copy nM and Assign QC flags

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

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 = Column

  • Placement Pattern = Column

• Destination Containers

  • BioAnalyzer DNA High Sensitivity Chip

  

  • BioAnalyzer DNA 1000 Chip

  

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Criteria 1 - Operator	Text Dropdown	Custom Entries	Presets >= <= = !=
  Criteria 1 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
  Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
  Criteria 2 - Operator	Text Dropdown	Custom Entries	Presets >= <= = !=
  Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
  Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2
  Use strict matching for Bioanalyzer results	Toggle Switch		Default = None Set

• Step File Placeholders

  • Bioanalyzer Input File - Automatically attached

  • Bioanalyzer Input File Generation Log File - Automatically attached

  • Bioanalyzer XML Result File (required) - Manually uploaded

  • Result File (optional) - Manually uploaded

  • PDF Summary File (optional) - Manually uploaded

  • Bioanalyzer XML Parsing Log File - Automatically attached

  • QC Assignment Log File - Automatically attached

  • QC Assignment Report - Automatically attached

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	BA Sample Name	Text
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Measurement	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Measurement	Number of Peaks found	Numeric		Decimal Places Displayed = 0
    Measurement	Number of Regions found	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Size - bp	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Molarity	Numeric		Decimal Places Displayed = 2

Step 5: Run Gel Electrophoresis and Recover Purified Construct (TruSeq Small RNA v1.0)

• Master Step Name = Run Gel Electrophoresis and Recover Purified Construct (TruSeq Small RNA v1.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • Novex TBE gels, 6%, 10 well

    • Supplier = Life Technologies

    • Catalog Number = EC6265BOX

  • Novex TBE running buffer (5X)

    • Supplier = Invitrogen

    • Catalog Number = LC6675

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

The version of Run Gel Electrophoresis and Recover Purified Construct 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
  70% EtOH Prep Date	Date

• Step File Placeholders

  • Gel Image - Manually uploaded

• 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 6: Concentrate Final Library (TruSeq Small RNA v1.0)

• Master Step Name = Concentrate Final Library (TruSeq Small RNA v1.0.10)

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {SubmittedSampleName}

• Reagent Kits

  • TruSeq Small RNA Library Prep Kit, Core Solutions

    • Supplier = Illumina

    • Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048

    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

The version of Concentrate Final Library master step name may be different depending on the version of IPP installed.

Automations

Calculate Master Mix for Pellet Paint

• 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 '(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 true -h false -exp 'if (step.::Is Pellet Paint being used?:: == ::Yes:: ) {(step.::Optional - Ultrapure water Volume (ul):: = step.::Total samples:: * 1.98) ; (step.::Optional - 1X Pellet Paint NF Co-Precipitant Volume (ul):: = step.::Total samples:: * 0.22) ; (step.::0.1X Pellet Paint Volume (ul):: = 2)}'  -log {compoundOutputFileLuid1}"

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
  Glycogen Volume (ul)	Numeric		Default = 2 Decimal Places Displayed = 0
  Is Pellet Paint being used?	Text Dropdown	Required Field	Presets Yes No
  Optional - 1X Pellet Paint NF Co-Precipitant Volume (ul)	Numeric		Decimal Places Displayed = 2
  Optional - Ultrapure water Volume (ul)	Numeric		Decimal Places Displayed = 2
  0.1X Pellet Paint Volume (ul)	Numeric		Decimal Places Displayed = 0
  70% EtOH Prep Date	Date
  3M NaOAc Volume (ul)	Numeric		Default = 30 Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - Automatically attached

  • 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 7: Bioanalyzer QC (Library Validation) (TruSeq Small RNA v1.0)

• Master Step Name = Bioanalyzer QC (Library Validation) v2.0

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

• 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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}  && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"

Parse Bioanalyzer XML, Calculate nM and assign QC flags

• 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 {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step - Output PASS/FAIL

• 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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Parse Bioanalyzer XML and assign QC flags

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML, Copy nM and Assign QC flags

• Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

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 = Column

  • Placement Pattern = Column

• Destination Containers

  • BioAnalyzer DNA High Sensitivity Chip

  

  • BioAnalyzer DNA 1000 Chip

  

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,500.00

Nextera Mate Pair Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Average Size - bp

• Criteria 2 - Threshold Value = 400.00

Nextera XT DNA Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 250.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

NRCC Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 350.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

TruSeq ChIP-Seq Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Average Size - bp

• Criteria 2 - Threshold Value = 400.00

TruSeq Exome Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

TruSeq Methyl Capture EPIC Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 200.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 200.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 500.00

TruSeq RNA Access Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 200.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 320.00

TruSeq RNA Exome Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 200.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 320.00

TruSeq Small RNA Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 100.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Average Size - bp

• Criteria 2 - Threshold Value = 200.00

TruSeq Stranded mRNA Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 250.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Average Size - bp

• Criteria 2 - Threshold Value = 275.00

TruSeq Stranded Total RNA Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 250.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Average Size - bp

• Criteria 2 - Threshold Value = 275.00

TruSeq Targeted RNA Expression Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 100.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 300.00

TruSight Myeloid Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Size - bp

• Criteria 2 - Threshold Value = 400.00

TruSight RNA Fusion Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 160.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Size - bp

• Criteria 2 - Threshold Value = 700.00

TSCA Library Validation

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Average Size - bp

• Criteria 1 - Threshold Value = 300.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Size - bp

• Criteria 2 - Threshold Value = 400.00

• Step Data

  • Group of Defaults = TruSeq Small RNA Library Validation

  • Master Step Fields

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Criteria 1 - Operator	Text Dropdown	Custom Entries	Presets >= <= = !=
    Criteria 1 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown	Custom Entries	Presets >= <= = !=
    Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Use strict matching for Bioanalyzer results	Toggle Switch		Default = None Set

• Step File Placeholders

  • Bioanalyzer Input File - Automatically attached

  • Bioanalyzer Input File Generation Log File - Automatically attached

  • Bioanalyzer XML Result File (required) - Manually uploaded

  • Result File (optional) - Manually uploaded

  • PDF Summary File (optional) - Manually uploaded

  • Bioanalyzer XML Parsing Log File - Automatically attached

  • QC Assignment Log File - Automatically attached

  • QC Assignment Report - Automatically attached

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	BA Sample Name	Text
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Measurement	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Measurement	Number of Peaks found	Numeric		Decimal Places Displayed = 0
    Measurement	Number of Regions found	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Size - bp	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Molarity	Numeric		Decimal Places Displayed = 2

Step 8: Normalize Libraries (TruSeq Small RNA v1.0)

• Master Step Name = Normalize Libraries 1 v2.0.10

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

The version of Normalize Libraries 1 master step name may be different depending on the version of IPP installed.

Automations

Normalization Calculations - Option 1

• 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.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}"

Set Next Step - Remove

• 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 = ::REMOVE::' -log {compoundOutputFileLuid0}"

Routing script - Normalize Libraries

• Trigger Location = Step

• Trigger Style = Automatic upon exit

bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq' \
--WORKFLOW 'MiSeq Sequencing v3.2' \
--STEP 'Library Pooling (MiSeq v3.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \
--STEP 'Library Pooling (NextSeq 500/550 v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 2.0' \
--WORKFLOW 'NovaSeq 6000 v2.3' \
--STEP 'Define Run Format (NovaSeq 6000 v2.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq 3.0' \
--WORKFLOW 'NovaSeq 6000 v3.8' \
--STEP 'Define Run Format (NovaSeq 6000 v3.8)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeqDx' \
--WORKFLOW 'NovaSeqDx v1.2' \
--STEP 'Define Run Format (NovaSeqDx v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000' \
--WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series v1.1' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
--WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
--STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The field value and actual version of the workflows and steps in the routing automation script 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
  Final Volume (ul)	Numeric	Required Field	Decimal Places Displayed = 2
  Target Normalization (nM)	Numeric	Required Field	Default = 2 Decimal Places Displayed = 2

• 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	Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Normalized Molarity (nM)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sequencing Instrument	Text Dropdown	Required Field	Presets MiSeq NextSeq NextSeq 1000/2000 NextSeq 1000/2000 On-Prem NovaSeq 2.0 NovaSeq 3.0 NovaSeq X Series NovaSeqDx
    Project	Project Name	Built-in

    ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP.