TruSeq RNA Exome v1.0

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

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 = 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
  80% EtOH Prep Date	Date
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • 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: Adenylate 3' Ends (TruSeq RNA Exome v1.0)

• Master Step Name = Adenylate 3' Ends v2.0

• Step Type = No Outputs

• Reagent Kits

  • 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 = 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
  ATL to add to each well (uL)	Numeric		Default = 12.5
  Comment	Multiline Text
  RSB to add to each well (uL)	Numeric		Default = 2.5
• Step File Placeholders

  • Log File - Automatically attached

• Sample Table

  • Sample Display Default = Expand

  • Well Sort Order = Column

  • 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 5: Ligate Adapters (TruSeq RNA Exome v1.0)

• Master Step Name = Ligate Adapters v2.0

• Step Type = Add Labels

• 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

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}"

Copy to Output

• 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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

Set Next Step & Copy to Input

• 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 {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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

Add Labels

• Label Groups

  • TruSeq RNA Single Indexes (12 indexes, 24 samples) Set A

  • TruSeq RNA Single Indexes (12 indexes, 24 samples) Set B

Record Details

• Step Data (Master Step Fields)

  Field Name	Field Type	Options	Additional Options and Dropdown Items
  Comment	Multiline Text
  Round 1 EtOH to each well (uL)	Numeric		Default = 42
  Round 1 RSB to each well (uL)	Numeric		Default = 52.5
  Round 2 EtOH to each well (uL)	Numeric		Default = 50
  Round 2 RSB to each well (uL)	Numeric		Default = 22.5
  1 RSB to add to each well (uL)	Numeric		Default = 2.5
  2 LIG to add to each well (uL)	Numeric		Default = 2.5
  3 RNA Adapters to add to each well (uL)	Numeric		Default = 2.5
  80% EtOH Prep Date	Date
• 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	Reagent Name	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: Enrich DNA Fragments (TruSeq RNA Exome v1.0)

• Master Step Name = Enrich DNA Fragments (TruSeq RNA Exome v1.0.6)

• 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 Enrichment Component, Box 1

    • Supplier = Illumina

    • Catalog Number = 20020490

    • Website = www.illumina.com

  • 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 = 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
  Thermal Cycler Program	Text		Default = PCR
  80% EtOH Prep Date	Date
• 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 7: Bioanalyzer QC (Library Validation) (TruSeq RNA Exome 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

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 RNA Exome 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: Hybridize Probes (TruSeq RNA Exome v1.0)

• Master Step Name = Hybridize with Pooling v2.0

• Step Type = Pooling

• Aliquot Generation = Fixed, 1

• Naming Convention = {PoolName}

• Reagent Kits

  • TruSeq RNA Library Prep Coding Exome Oligos

    • Supplier = Illumina

    • Catalog Number = 20020183

    • Website = www.illumina.com

  • TruSeq RNA Library Prep Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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

Pooling

• Label Uniqueness = On

• Defaults

  • Sample Grouping = Group by Containers

  • Well Sort Order = Row

Placement = Enabled

• Defaults

  • Well Sort Order = Row

  • Placement Pattern = Column

• 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 Dropdown	Custom Entries	Presets RNA HYB NRC HYB
• 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 9: Capture Hybridized Probes (TruSeq RNA Exome v1.0)

• Master Step Name = Capture Hybridized Probes v2.0

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq RNA Library Prep Enrichment Component, Box 1

    • Supplier = Illumina

    • Catalog Number = 20020490

    • Website = www.illumina.com

  • TruSeq RNA Library Prep Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • Website = www.illumina.com

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::Total Number of Samples:: = step.::Total Number of Samples:: + 1' -log {compoundOutputFileLuid0} && /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.::Enrichment Elution Buffer 1 (ul):: = 28.5 * step.::Total Number of Samples:: ; step.::2N NaOH (ul):: = 1.5 * step.::Total Number of 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 = 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
  Enrichment Elution Buffer 1 (ul)	Numeric		Decimal Places Displayed = 2
  2N NaOH (ul)	Numeric		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	Sample Name	Built-in
    Project	Project Name	Built-in

Step 10: Second Hybridization (TruSeq RNA Exome v1.0)

• Master Step Name = Perform Second Hybridization v2.0

• Step Type = No Outputs

• Reagent Kits

  • TruSeq RNA Library Prep Coding Exome Oligos

    • Supplier = Illumina

    • Catalog Number = 20020183

    • Website = www.illumina.com

  • TruSeq RNA Library Prep Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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
  Thermal Cycler Program RNA Exome	Text		Default = RNA HYB
• 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 11: Second Capture (TruSeq RNA Exome v1.0)

• Master Step Name = Perform Second Capture v2.0

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• Reagent Kits

  • TruSeq RNA Library Prep Enrichment Component, Box 1

    • Supplier = Illumina

    • Catalog Number = 20020490

    • Website = www.illumina.com

  • TruSeq RNA Library Prep Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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
• 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 12: Clean Up Captured Library (TruSeq RNA Exome v1.0)

• Master Step Name = Clean Up v2.0

• Step Type = Standard

• Derived Sample Generation = Fixed, 1

• Naming Convention = {InputItemName}

• 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 Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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
  80% EtOH Prep Date	Date
• 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 13: Amplify Enriched Library (TruSeq RNA Exome v1.0)

• Master Step Name = Second PCR Amplification v1.0

• Step Type = No Outputs

• Reagent Kits

  • TruSeq RNA Library Prep Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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
  Thermal Cycler Program	Text		Default = EPM AMP
• 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 14: Clean Up Amplified Enriched Library (TruSeq RNA Exome v1.0)

• Master Step Name = Clean Up v2.0

• Step Type = Standard

• 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 Enrichment Component, Box 2

    • Supplier = Illumina

    • Catalog Number = 20020490

    • 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 = 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
  80% EtOH Prep Date	Date
• 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 15: Bioanalyzer QC (Library Validation) (TruSeq RNA Exome 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 RNA Exome 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