Illumina DNA PCR-Free Library Prep Manual v1.1

Overview

The Illumina DNA PCR-Free Library Prep Manual workflow includes the following functionality.

  • Preset Illumina DNA PCR-Free Library Prep Manual protocols that support the preparation of up to 96 dual-indexed paired-end single-stranded libraries from DNA using the Illumina DNA PCR-Free Library Prep workflow.

  • Automated calculation of sample and buffer volumes.

  • Automated calculation or display of reagents at every step in the protocol.

  • Automatic step transition when required.

  • Automatic placement of samples when necessary.

  • Automated assignment of QC Pass/Fail, based on user-selected threshold values.

Protocol 1: Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Sort Sample (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = No Outputs

The version of Sort Sample master step name may be different depending on the version of IPP installed.

Automations

Set Next Step - DNA PCR-Free Lib Prep
  • 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 'if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::gDNA:: && input.::Protocol Type:: == ::Hybex::) {nextStep = ::Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Whole Blood:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Dried Blood Spot:: && input.::Protocol Type:: == ::Thermal Cycler::) {nextStep = ::Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type for DNA PCR-Free Lib Prep:: == ::Saliva:: && input.::Protocol Type::  == ::Thermal Cycler::) {nextStep = ::Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

ℹ The version of the nextStep step names may be different depending on the version of IPP installed.

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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction Notes

    Multiline Text

    Read Only

    Default = Select a sample type and protocol type for each sample.

  • Step File Placeholders

    • Log - 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

      Protocol Type

      Text Dropdown

      Required Field

      • Presets

        • Thermal Cycler

        • Hybex

      • Default = Thermal Cycler

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type for DNA PCR-Free Lib Prep

      Text Dropdown

      Required Field

      • Presets

        • gDNA

        • Whole Blood

        • Dried Blood Spot

        • Saliva

      • Default = gDNA

      Project

      Project Name

      Built-in

Step 2: Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Qubit - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Qubit - Hybex master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep
  • 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 'output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"
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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Set Next Step-REMOVE and Copy Concentration & Sample Type
  • 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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ; input.::Sample Type:: = output.::Sample Type::' -log {compoundOutputFileLuid0}"
Routing - gDNA Hybex
  • 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 'Sample Type' \
--FIELD_VALUE 'gDNA' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Criteria 1 - Operator

    Text

    • Default = >=

    Criteria 1 - Source Data Field

    Text

    • Default = Concentration

    Criteria 1 - Threshold Value

    Numeric

    • Default = 300

    • Range = 300 To 2000

    Criteria 2 - Operator

    Text

    • Default = <=

    Criteria 2 - Source Data Field

    Text

    • Default = Concentration

    Criteria 2 - Threshold Value

    Numeric

    • Default = 2000

    • Range = 300 To 2000

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Upload or enter Concentration and Conc. Units. 2. Set Threshold Values then click on Assign QC Flags.

  • Step File Placeholders

    • Log - Automatically attached

    • QC Log File - Automatically attached

    • QC Result File - Automatically attached

    • Upload File - Manually uploaded

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • 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

      Concentration

      Numeric

      • Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      • Required Field

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Measurement

      Concentration

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Conc. Units

      Text

      Measurement

      Sample Type

      Text

      Project

      Project Name

      Built-in

Step 3: Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Qubit - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Qubit - Thermal Cycler master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep
  • 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 'output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-log {compoundOutputFileLuid0}"
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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Set Next Step-REMOVE, Set Prep Input Type, Copy Concentration & Sample Type
  • 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 -exp 'nextStep = ::REMOVE:: ; \
if (output.::Concentration:: >= 25 && output.::Concentration:: <= 99) {output.::Prep Input Type:: = ::Low::} ; \
if (output.::Concentration:: >= 100 && output.::Concentration:: <= 2000) {output.::Prep Input Type:: = ::Standard::} ; \
input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units:: ; input.::Sample Type:: = output.::Sample Type::' -log {compoundOutputFileLuid0}"
Routing - gDNA Thermal Cycler
  • Trigger Location = Step

  • 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'INPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Criteria 1 - Operator

    Text

    Default = >=

    Criteria 1 - Source Data Field

    Text

    Default = Concentration

    Criteria 1 - Threshold Value

    Numeric

    Default = 25

    Criteria 2 - Operator

    Text

    Default = <=

    Criteria 2 - Source Data Field

    Text

    Default = Concentration

    Criteria 2 - Threshold Value

    Numeric

    Default = 2000

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Upload or enter Concentration and Conc. Units. 2. Set Threshold Values then click on Assign QC Flags.

  • Step File Placeholders

    • Log - Automatically attached

    • QC Log File - Automatically attached

    • QC Result File - Automatically attached

    • Upload File - Manually uploaded

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • 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

      Concentration

      Numeric

      • Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      • Required Field

      Derived Sample

      Prep Input Type

      Text

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Measurement

      Concentration

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Conc. Units

      Text

      Measurement

      Prep Input Type

      Text

      Measurement

      Sample Type

      Text

      Project

      Project Name

      Built-in

Step 4: Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Whole Blood Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina Lysis Reagent Kit

The version of Whole Blood Lysis master step name may be different depending on the version of IPP installed.

Automations

Calculate Whole Blood Lysis Master Mix & Copy Sample Type
  • 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 ; \
step.::MLB (uL):: = step.::Total Samples:: * 30 *1.1 ; \
step.:: PK1 (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.:: Nuclease-free water (uL):: = step.::Total Samples:: * 248 * 1.1 ; \
output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep::' \
-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 - Whole Blood Lysis
  • Trigger Location = Step

  • 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'Whole Blood' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Combine MLB, PK1 and Nuclease-free water to create the Lysis Master Mix in a 15 mL tube. 2. Add 280 µl of lysis master mix to a new 2 mL tube. 3. Add 20 uL to each 2 mL tube, mix by pipetting then vortex briefly and centrifuge. 4. Incubate and shake at 1000 rpm for 15 mins then centrifuge briefly. 5. Add 135 uL of IPB, invert tube, vortex for 15 secs to mix. 6. Incubate at RT for 5 mins. 7. Place tube on magnetic stand for 5 mins then remove and discard supernatant. 8. Wash beads 2x with 500 uL of fresh 80% EtOH for each wash. 9. Air dry on magnetic stand for 5 mins. 10. Add 35 uL of RSB to each tube and vortex to mix. 11. Label a new 96 well PCR plate with LP1 and add 32 uL of supernatant of each sample to a new well.

    MLB (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Nuclease-free water (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    PK1 (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Total Samples

    Numeric

    Read Only

    • Default = 0

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Step 5: Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Dried Blood Spot Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina Lysis Reagent Kit

The version of Dried Blood Spot Lysis master step name may be different depending on the version of IPP installed.

Automations

Calculate Dried Blood Lysis Master Mix
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::10x Lysis Buffer (uL):: = step.::Total Samples:: * 30 *1.1 ; \
step.:: PK1 (uL):: = step.::Total Samples:: * 2 * 1.1 ; \
step.:: Nuclease-free water (uL):: = step.::Total Samples:: * 268 * 1.1 ; \
output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep::' \
-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 - Dried Blood Spot Lysis
  • Trigger Location = Step

  • 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'Dried Blood Spot' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    10x Lysis Buffer (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    80% EtOH Prep Date

    Date

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Combine 10x Lysis Buffer, PK1 and Nuclease-free water to create the Lysis Master Mix in a 15 mL tube. 2. Add 300 uL of lysis master mix to a new 2 mL tube. 3. Add 6 x 3 mm² punches to a each 2 ml tube, mix by pipetting then vortex briefly and centrifuge. 4. Incubate and shake at 1000 rpm for 15 mins then centrifuge briefly. 5. Without removing the punches, transfer all supernatant from each tube to a new 2 ml tube. 6. Add 135 uL of IPB, invert tube, vortex for 15 secs to mix. 7. Incubate at RT for 5 mins. 8. Place tube on magnetic stand for 5 mins then remove and discard supernatant. 9. Wash beads 2x with 500 uL of fresh 80% EtOH for each wash. 10. Air dry on magnetic stand for 5 mins. 11. Add 35 uL of RSB to each tube and vortex to mix. 12. Incubate at RT for 2 mins then on the magnetic stand until the liquid turns clear. 13. Label a new 96 well PCR plate with LP1 and add 32 uL of supernatant of each sample to a new well.

    Nuclease-free water (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    PK1 (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Total Samples

    Numeric

    Read Only

    • Default = 0

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Step 6: Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Saliva Lysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina Lysis Reagent Kit

The version of Saliva Lysis master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type for DNA PCR-Free Lib Prep
  • 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 'output.::Sample Type:: = input.::Sample Type for DNA PCR-Free Lib Prep:: ' \
-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 - Saliva Lysis
  • Trigger Location = Step

  • 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 -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'Saliva' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Incubate saliva overnight at 50°C in a water bath or air incubator. 2. Add 250 uL of Nuclease-Free Water to a new 2 mL tube. 3. Invert each heat-treated saliva collection tube 5 times to mix, add 50 uL of Saliva to each 2 mL tube, pipette to mix, vortex briefly and then centrifuge. 4. Add 135 uL of IPB, invert tube, vortex for 15 secs to mix. 5. Incubate at RT for 5 mins. 6. Place tube on magnetic stand for 5 mins then remove and discard supernatant. 7. Wash beads 2x with 500 uL of fresh 80% EtOH for each wash. 8. Air dry on magnetic stand for 5 mins. 9. Add 35 uL of RSB to each tube and vortex to mix. 10. Incubate at RT for 2 mins then on the magnetic stand until the liquid turns clear. 11. Label a new 96 well PCR plate with LP1 and add 32 uL of supernatant of each sample to a new well.

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Derived Sample

      Sample Type

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Protocol 2: Library Prep - Hybex (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Tagment Genomic DNA (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Tagment Genomic DNA master step name may be different depending on the version of IPP installed.

Automations

Copy Concentration
  • 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 'output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' \
-log {compoundOutputFileLuid0}"
Calculate DNA Volume & Copy Desired DNA Input
  • 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false \
-exp 'output.::DNA (uL):: = (step.::Desired DNA Input (ng):: / output.::Concentration::) ; \
output.::RSB (uL):: = (25 - output.::DNA (uL)::) ; \
output.::Desired DNA Input (ng):: = step.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Desired DNA Input (ng)

    Numeric

    • Range = 300 To 2000

    • Decimal Places Displayed = 0

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Label a new 96 well MIDI plate with LP1 and add the calculated DNA and RSB volumes of each sample to a new well on the plate. 2. Add 10 uL of TB1 to each well. 3. Add 15 uL of BLT-PF to each well. 4. Seal and shake at 1800 rpm for 1 minute. 5. Incubate in pre-heated Hybex for 8 minutes.

  • Step File Placeholders

    • Log - 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

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      Required Field

      Derived Sample

      Desired DNA Input (ng)

      Numeric Dropdown

      Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      DNA (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      RSB (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = No Outputs

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Post Tagmentation Cleanup master step name may be different depending on the version of IPP installed.

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 Desired DNA 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Add 10 µl ST2 to each well then seal and shake at 1800 rpm for 1 minute. 2. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 3. Without disturbing the bead pellet, remove and discard all supernatant from each well. 5. Add 150 μl TWB to each well then seal and shake at 1800 rpm for 1 minute. 6. Place on the magnetic stand and wait until the liquid is clear (~2 minutes).

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 3: Ligate Indexes (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Ligate Indexes (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Add Labels

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}-{AppliedReagentLabels}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

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

Automations

Calculate Dilution for HP3 & Copy Desired DNA Input
  • 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng):: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 6 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 54' \
-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

    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

    • 96 well plate

Add Labels

  • Label Groups

    • IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • Illumina DNA-RNA UD Indexes Set A B C D Tagmentation

    • Illumina DNA-RNA UD Indexes Set A Tagmentation

    • Illumina DNA-RNA UD Indexes Set B Tagmentation

    • Illumina DNA-RNA UD Indexes Set C Tagmentation

    • Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    HP3 (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Instruction Notes for Hybex Protocol

    Multiline Text

    Read Only

    • Default = 1. Remove and discard all supernatant. 2. Add 45 µl ELM to each well. 3. Add 5 µl index adapters to each well then seal and shake at 1800 rpm for 1 min. 4. Incubate in the preheated Hybex for 8 mins. 5. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 6. Remove and discard all supernatant from each well. 7. Add 75 µl TWB onto the beads in each well then seal and shake at 1800 rpm for 1 minute. 8. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 9. Remove and discard all supernatant from each well. 10. Without disturbing the bead pellet, use a 20 µl pipette to remove and discard residual TWB from each well. 11. Add 45 µl diluted HP3 to each well then seal and shake at 1800 rpm for 1 minute.

    Nuclease-free water (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Total Samples

    Numeric

    Read Only

    • Default = 0

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 4: Clean Up Libraries (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Clean Up Libraries (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

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

Automations

Copy Desired DNA Input
  • 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"
Set Next Step-Remove & Prep Input Type
  • 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 -exp 'nextStep = ::REMOVE:: ; \
output.::Prep Input Type:: = ::Standard::' -log {compoundOutputFileLuid0}"
Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Add 36 µl IPB to each well then seal and shake at 1800 rpm for 1 minute. 2. Incubate at room temperature for 2 minutes. 3. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 4. Label a new 96-well MIDI plate LP2. 5. Add 42 µl IPB to each well of LP2. 6. Without disturbing the bead pellet, transfer 76 µl supernatant from each well of LP1 to the corresponding well of LP2 then seal and shake at 1800 rpm for 1 minute. 7. Discard LP1 and incubate LP2 at room temperature for 2 minutes. 8. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 9. Without disturbing the bead pellet, remove and discard all supernatant from each well. 10. Wash beads 2x with 180 uL of fresh 80% EtOH for each wash. 11. Using a 20 µl pipette, remove residual EtOH from each well. 12. Air-dry on the magnetic stand (~4 minutes). 13. Add 22 µl of RSB onto the beads in each well then seal and shake at 1800 rpm for 1 minute. 14. Incubate at room temperature for 2 minutes. 15. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 16. Label a new PCR plate FLP. 17. Transfer 20 µl supernatant from each well of LP2 to the corresponding well of FLP.

  • Step File Placeholders

    • Log - 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

      Desired DNA Input (ng)

      Numeric Dropdown

      Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Prep Input Type

      Text

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 3: Library Prep - Thermal Cycler Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Tagment Genomic DNA - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Tagment Genomic DNA - Standard Input v1.0.2

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Tagment Genomic DNA - Standard Input master step name may be different depending on the version of IPP installed.

Automations

Copy Sample Type & Concentration
  • 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 'output.::Sample Type:: = input.::Sample Type:: ; \
if (output.::Sample Type:: == ::gDNA::) {output.::Concentration:: = input.::Concentration::} else {output.::Concentration:: = 0} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::Conc. Units:: = input.::Conc. Units::} else {output.::Conc. Units:: = ::NA::}' \
-log {compoundOutputFileLuid0}"
Calculate Dilution & BLT-PF Volumes and Copy Desired DNA Input
  • 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 false \
-h false \
-exp 'output.::Desired DNA Input (ng):: = step.::Desired DNA Input (ng):: ; \
if (output.::Sample Type:: == ::gDNA::) {output.::DNA (uL):: = output.::Desired DNA Input (ng):: / output.::Concentration::} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::DNA (uL):: = 30} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::RSB (uL):: = 25 - output.::DNA (uL)::} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::RSB (uL):: = 0} ; \
if (output.::Sample Type:: == ::gDNA::) {output.::BLT-PF (uL):: = 15} ; \
if (output.::Sample Type:: == ::Whole Blood::) {output.::BLT-PF (uL):: = 10} ; \
if (output.::Sample Type:: == ::Dried Blood Spot::) {output.::BLT-PF (uL):: = 10} ; \
if (output.::Sample Type:: == ::Saliva::) {output.::BLT-PF (uL):: = 10}' \
-log {compoundOutputFileLuid0}"
Set Next Step-Post TAG
  • 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 \
-exp 'if (input.::Sample Type:: == ::Whole Blood::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::Dried Blood Spot::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::Saliva::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (input.::Sample Type:: == ::gDNA::) {nextStep = ::Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-log {compoundOutputFileLuid0}"

ℹ The actual version of the nextStep step names may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Desired DNA Input (ng)

    Numeric

    Required Field

    Range = 100 To 2000

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Label a new 96 well PCR plate LP1. 2. Add the calculated DNA, and RSB volumes to the LP1 plate and then pipette to mix. 3. Add the calculated BLT-PF to each well and pipette to mix. 4. Add 10 uL of TB1 to each well, pipette to mix and then seal. 5. Place the LP1 plate on the thermo cycler and run the TAG program.

    Thermal Cycler Program

    Text

    Default = TAG

    Thermal Cycler Program Notes

    Multiline Text

    Read Only

    Default = 1. Choose the preheat lid option and set to 100°C 2. Set the reaction volume to 50 µl u 41°C for 5 minutes.

  • Step File Placeholders

    • Log - 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

      BLT-PF (uL)

      Numeric

      Derived Sample

      Concentration

      Numeric

      • Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      • Required Field

      Derived Sample

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      DNA (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      RSB (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Requird Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Step 2: Tagment Genomic DNA - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Tagment Genomic DNA - Low Input v1.0

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

Automations

Calculate Tag Master Mix and Copy Concentration & Sample Type
  • 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 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Sample Type:: = input.::Sample Type:: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::BLT-PF (uL):: = step.::Total Samples:: * 11 ; \
step.::TB1 (uL):: = step.::Total Samples:: * 11' \
-log {compoundOutputFileLuid0}"
Calculate Dilution and Copy Desired DNA Input
  • 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 false \
-h false \
-exp 'output.::Desired DNA Input (ng):: = step.::Desired DNA Input (ng):: ; \
output.::DNA (uL):: = output.::Desired DNA Input (ng):: / output.::Concentration:: ; \
output.::RSB (uL):: = 30 - output.::DNA (uL)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    BLT-PF (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Desired DNA Input (ng)

    Numeric

    Required Field

    • Default = 25

    • Range = 25 To 99</li

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Label a new 96 well MIDI plate LP1. 2. Combine the calculated BLT-PF and TB1 volumes into a 1.5 mL tube to prepare the Tagmentation Master Mix. 3. Add the calculated DNA, and RSB volumes to the LP1 plate and then pipette to mix. 4. Add 20 µl Tagmentation Master Mix to each well, pipette to mix and then seal. 5. Place the LP1 plate on the thermo cycler and run the TAG program.

    TB1 (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Thermal Cycler Program

    Text

    • Default = TAG

    Thermal Cycler Program Notes

    Multiline Text

    Read Only

    • Default = 1. Choose the preheat lid option and set to 100°C 2. Set the reaction volume to 50 µl u 41°C for 5 minutes.

    Total Samples

    Numeric

    Read Only

    • Default = 0

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log - 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

      Concentration

      Numeric

      • Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      • Required Field

      Derived Sample

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      DNA (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      RSB (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Requird Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Step 3: Post Tagmentation Cleanup (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Post Tagmentation Cleanup v1.0.1

  • Step Type = No Outputs

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Post Tagmentation Cleanup master step name may be different depending on the version of IPP installed.

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 Desired DNA Input & Sample Type
  • 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.::Sample Type:: = input.::Sample Type:: ; \
output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Add 10 µl ST2 to each well, seal and then shake at 1800 rpm for 1 minute. 2. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 3. Without disturbing the bead pellet, remove and discard all supernatant from each well. 4. Add 150 μl TWB to each well, seal and shake at 1800 rpm for 1 minute. 5. Place on the magnetic stand and wait until the liquid is clear (~2 minutes).

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample Type

      Text Dropdown

      • Requird Field

      • Custom Entries

      Presets

      • DNA

      • RNA

      Project

      Project Name

      Built-in

Step 4: Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Add Labels

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}-{AppliedReagentLabels}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Ligate Indexes - Thermal Cycler (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

Automations

Calculate Dilution for HP3 & Copy Desired DNA Input
  • 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng):: ; \
step.::Total Samples:: = step.::Total Samples:: + 1 ; \
step.::HP3 (uL):: = step.::Total Samples:: * 6 ; \
step.::Nuclease-free water (uL):: = step.::Total Samples:: * 54' \
-log {compoundOutputFileLuid0}"
Set Next Step - Clean Up Libraries
  • 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 \
-exp 'if (output.::Desired DNA Input (ng):: >= 100) {nextStep = ::Clean Up Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::} ; \
if (output.::Desired DNA Input (ng):: <= 99) {nextStep = ::Clean Up Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)::}' \
-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

    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

Add Labels

  • Label Groups

    • IDT for Illumina Nextera DNA UD Indexes Set A for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set A-D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set B for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set C for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • IDT for Illumina Nextera DNA UD Indexes Set D for NovaSeq, MiSeq, HiSeq 2500 and HiSeq 2000

    • Illumina DNA-RNA UD Indexes Set A B C D Tagmentation

    • Illumina DNA-RNA UD Indexes Set A Tagmentation

    • Illumina DNA-RNA UD Indexes Set B Tagmentation

    • Illumina DNA-RNA UD Indexes Set C Tagmentation

    • Illumina DNA-RNA UD Indexes Set D Tagmentation

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    HP3 (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Remove and discard all supernatant. 2. Add 45 µl ELM to each well and pipette to mix. 3. Add 5 µl index adapters to each well then seal and shake at 1800 rpm for 1 min. 4. Place on the preprogrammed thermal cycler and run the ELM program. 5. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 6. Remove and discard all supernatant from each well. 7. Add 75 µl TWB onto the beads in each well then pipette to mix. 8. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 9. Remove and discard all supernatant from each well. 10. Seal and centrifuge at 280 x g for 10 seconds and then place on magnetic stand. 11. Without disturbing the bead pellet, remove and discard residual TWB from each well. 12. Remove the plate from the magnetic stand. 13. Add 45 µl diluted HP3 to each well, pipette to mix and then incubate at RT for 2 mins.

    Nuclease-free water (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 0

    Thermal Cycler Program

    Text

    • Default = ELM

    Thermal Cycler Program Notes

    Multiline Text

    Read Only

    • Default = ELM Program 1. Choose the preheat lid option and set to 100°C 2. Set the reaction volume to 50 μl 3. Run for 37°C for 5 minutes 4. Run for 50°C for 5 minutes

    Total Samples

    Numeric

    Read Only

    • Default = 0

    • Decimal Places Displayed = 0

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 5: Clean Up Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Clean Up Libraries - Thermal Cycler v1.0.2

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Clean Up Libraries - Thermal Cycler master step name may be different depending on the version of IPP installed.

Automations

Copy Desired DNA Input
  • 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"
Set Next Step-Remove & Prep Input Type
  • 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 -exp 'nextStep = ::REMOVE:: ; \
if (output.::Desired DNA Input (ng):: >= 300) {output.::Prep Input Type:: = ::Standard::} else {output.::Prep Input Type:: = ::Low::}' \
-log {compoundOutputFileLuid0}"
Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Instruction Notes for Standard Input

    Multiline Text

    Read Only

    Default = 1. Add 36 µl IPB to each well containing BLT-PF beads and pipette to mix. 2. Incubate at room temperature for 2 minutes. 3. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 4. Label a new 96-well PCR plate LP2. 5. Add 42 µl IPB to each well of LP2. 6. Without disturbing the bead pellet, transfer 76 µl supernatant from each well of LP1 to the corresponding well of the LP2, pipette to mix and remove LP1 from the magnetic stand, and then discard. 7. Incubate LP2 at room temperature for 2 minutes. 8. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 9. Without disturbing the bead pellet, remove and discard all supernatant from each well. 10. Wash beads 2x with 180 µl fresh 80% ethanol per well for each wash. 11. Seal and then centrifuge 280 x g for 10 seconds. 12. Place on the magnetic stand, and then wait 10 seconds. 13. Remove residual EtOH from each well, air-dry on the magnetic stand (~2 minutes) then remove from the magnetic stand. 14. Add 22 µl RSB onto the beads in each well and pipette to mix. 15. Incubate at room temperature for 2 minutes. 16. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 17. Label a new PCR plate FLP. 18. Transfer 20 µl supernatant from each well of LP2 to the corresponding well of FLP.

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Prep Input Type

      Text

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 6: Clean Up Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Clean Up Libraries - Thermal Cycler v1.0.2

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Clean Up Libraries - Thermal Cycler master step name may be different depending on the version of IPP installed.

Automations

Copy Desired DNA Input
  • 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 'output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::' \
-log {compoundOutputFileLuid0}"
Set Next Step-Remove & Prep Input Type
  • 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 -exp 'nextStep = ::REMOVE:: ; \
if (output.::Desired DNA Input (ng):: >= 300) {output.::Prep Input Type:: = ::Standard::} else {output.::Prep Input Type:: = ::Low::}' \
-log {compoundOutputFileLuid0}"
Routing - Quantify & Pool 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 'Prep Input Type' \
--FIELD_VALUE 'Standard' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'Prep Input Type' \
--FIELD_VALUE 'Low' \
--WORKFLOW 'Illumina DNA PCR-Free Library Prep Manual v1.0.3' \
--STEP 'KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"

ℹ The actual version of the workflow and step names for the routing script may be different depending on the version of IPP installed.

Set Next Step - Advance
  • 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::' \
      -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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    80% EtOH Prep Date

    Date

    Instruction Notes for Low Input

    Multiline Text

    Read Only

    Default = 1. Add 81 µl IPB to each well and pipette to mix. 2. Incubate at room temperature for 5 minutes. 3. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 4. Remove and discard all supernatant from each well. 5. Wash beads 2x with 180 uL of fresh 80% EtOH for each wash. 6. Seal plate then centrifuge 280 x g for 10 seconds. 7. Place on the magnetic stand and wait until the liquid is clear (~5 minutes). 8. Remove residual EtOH from each well and air-dry on the magnetic stand (~2 minutes). 9. Remove the plate from the magnetic stand. 10. Add 15 µl RSB onto the beads in each well and pipette to resuspend. 11. Incubate at room temperature for 2 minutes. 12. Place on the magnetic stand and wait until the liquid is clear (~2 minutes). 13. Transfer 14 µl supernatant from each well of the plate to the corresponding well of a new PCR plate.

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Prep Input Type

      Text

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Protocol 4: Quantify and Pool Libraries - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Pool Samples - Standard Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Pool Samples (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

  • Reagent Kits

    • Illumina DNA PCR-Free Library Prep

      • Supplier = Illumina

      • Catalog Number = 24 - 20041794; 96 - 20041795

The version of Pool Samples (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

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

    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

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Combine 9 µl of each library in a 1.5 or 1.7 ml microcentrifuge tube. 2. Vortex to mix, and then centrifuge at 280 x g for 1 minute.

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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 2: Qubit (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Qubit (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

The version of Qubit (Illumina DNA PCR-Free Library Prep Manual) master step name may be different depending on the version of IPP installed.

Automations

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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Set Next Step-Remove and Copy Concentration
  • 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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Criteria 1 - Operator

    Text

    Default = >=

    Criteria 1 - Source Data Field

    Text

    Default = Concentration

    Criteria 1 - Threshold Value

    Numeric

    Criteria 2 - Operator

    Text

    Default = <=

    Criteria 2 - Source Data Field

    Text

    Default = Concentration

    Criteria 2 - Threshold Value

    Numeric

  • Step File Placeholders

    • Log - Automatically attached

    • QC Log File - Automatically attached

    • QC Result File - Automatically attached

    • Upload File - Manually uploaded

  • 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

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Concentration

      Numeric

      Required Field

      Decimal Places Displayed = 2

      Derived Sample

      Conc. Units

      Text

      Required Field

      Derived Sample

      Sample Name

      Built-in

      Measurement

      Concentration

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Conc. Units

      Text

      Project

      Project Name

      Built-in

Protocol 5: Quantify and Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: KAPA Sample Prep (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = KAPA Sample Prep - Illumina/Universal v1.0.1

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • 0.05% Tween® 20

    • 10 mM Tris-HCl, pH 8.0 – 8.5 (25°C)

  • Control Types

    • KAPA DNA Standard 1

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 20 pM

      • Control Use

        • Single step only = No

    • KAPA DNA Standard 2

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 2 pM

      • Control Use

        • Single step only = No

    • KAPA DNA Standard 3

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 0.2 pM

      • Control Use

        • Single step only = No

    • KAPA DNA Standard 4

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 0.02 pM

      • Control Use

        • Single step only = No

    • KAPA DNA Standard 5

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 0.002 pM

      • Control Use

        • Single step only = No

    • KAPA DNA Standard 6

      • Supplier = Roche

      • Catalog Number = KK4828-07960166001

      • Website = www.roche.com

      • Conc. = 0.0002

      • Control Use

        • Single step only = No

    • KAPA Library Quantification Dilution Control

      • Supplier = Roche

      • Catalog Number = KK4906

      • Website = www.roche.com

      • Conc. = 200 pM

      • Control Use

        • Single step only = No

    • KAPA NTC

      • Control Use

        • Single step only = No

The version of KAPA Sample Prep - Illumina/Universal master step name may be different depending on the version of IPP installed.

Automations

Copy Desired DNA Input for KAPA
  • 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 'if (output.name.contains(::KAPA DNA Standard 1::)) {output.::Desired DNA Input (ng):: = 0.005952} ; \
if (output.name.contains(::KAPA DNA Standard 2::)) {output.::Desired DNA Input (ng):: = 0.000595}  ; \
if (output.name.contains(::KAPA DNA Standard 3::)) {output.::Desired DNA Input (ng):: = 0.00006}  ; \
if (output.name.contains(::KAPA DNA Standard 4::)) {output.::Desired DNA Input (ng):: = 0.000006}  ; \
if (output.name.contains(::KAPA DNA Standard 5::)) {output.::Desired DNA Input (ng):: = 0.0000006}  ; \
if (output.name.contains(::KAPA DNA Standard 6::)) {output.::Desired DNA Input (ng):: = 0.00000006}  ; \
if (output.name.contains(::KAPA Library Quantification Dilution Control::)) {output.::Desired DNA Input (ng):: = 0.059524} ; \
if (output.name.contains(::KAPA NTC::)) {output.::Desired DNA Input (ng):: = 0} ; \
if (!output.name.contains(::KAPA::)) {output.::Desired DNA Input (ng):: = input.::Desired DNA Input (ng)::}' \
-log {compoundOutputFileLuid0}"
Calculate Expected Concentration & Dilution Factor
  • 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false \
-exp 'output.::Expected Concentration (pM):: = output.::Desired DNA Input (ng):: * 3.36 * 1000 ; \
if (output.::Expected Concentration (pM):: >= 84000 && output.::Expected Concentration (pM):: <= 188000) {output.::Dilution Factor:: = 10000} ; \
if (output.::Expected Concentration (pM):: >= 189000 && output.::Expected Concentration (pM):: <= 333000) {output.::Dilution Factor:: = 20000} ; \
if (output.::Expected Concentration (pM):: <= 83000) {output.::Dilution Factor:: = 0}' \
-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 true -h false \
-exp 'if (output.::Expected Concentration (pM):: > 333000) {fail(::Expected Concentration is too high, please edit Dilution Factor and recalculate::)}' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    DNA Dilution Buffer Prep Date

    Date

    Instruction Notes

    Multiline Text

    Read Only

    Default = - Prepare the appropriate library dilutions (using DNA dilution buffer). - Depending on the expected concentration of the library, 1:1,000 – 1:100,000 dilutions may be appropriate.

  • Step File Placeholders

    • Log - 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

      Desired DNA Input (ng)

      Numeric Dropdown

      • Custom Entries

      Presets

      • 99

      • 50

      • 25

      • 0.005952

      • 0.000595

      • 0.00006

      • 0.000006

      • 6e-7

      • 6e-8

      • 0.059524

      Derived Sample

      Dilution Factor

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • 1:10000

      • 1:20000

      Derived Sample

      Expected Concentration (pM)

      Numeric

      Decimal Places Displayed = 4

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 2: KAPA qPCR Prep & Analysis (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = KAPA qPCR Prep & Analysis - Illumina/Universal v1.0

  • Step Type = Standard QC

  • Measurement Generation = Variable

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • KAPA qPCR library quantification kit - Illumina/Universal

      • Supplier = Roche

      • Catalog Number = 07960166001

      • Website = www.roche.com

Automations

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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Calculate Average Cq
  • 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:computeReplicateAverage \
 -src 'Cq' \
 -dest 'Average Cq' \
 -log {compoundOutputFileLuid0}"
Calculate qPCR Master Mix & Sample Volume
  • 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 ; \
if (step.::Reaction Volume (uL):: == 20) {step.::KAPA SYBR FAST qPCR Master Mix + Primer Premix (uL):: = step.::Total Samples:: * 12} else {step.::KAPA SYBR FAST qPCR Master Mix + Primer Premix (uL):: = step.::Total Samples:: * 6} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::Yes::) {step.::ROX (uL):: = step.::Total Samples:: * 0.4} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::No::) {step.::ROX (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::Yes::) {step.::ROX (uL):: = step.::Total Samples:: * 0.2} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::No::) {step.::ROX (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::Yes::) {step.::PCR-grade water (uL):: = step.::Total Samples:: * 3.6} ; \
if (step.::Reaction Volume (uL):: == 20 && step.::Adding Rox?:: == ::No::) {step.::PCR-grade water (uL):: = step.::Total Samples:: * 4} ; \
if (step.::Reaction Volume (uL):: == 10) {step.::PCR-grade water (uL):: = 0} ; \
if (step.::Reaction Volume (uL):: == 20) {output.::qPCR master mix (uL):: = 16} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::Yes::) {output.::qPCR master mix (uL):: = 6.2} ; \
if (step.::Reaction Volume (uL):: == 10 && step.::Adding Rox?:: == ::No::) {output.::qPCR master mix (uL):: = 6} ; \
output.::Sample (uL):: = 4' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

    • 96 well plate

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Adding Rox?

    Text Dropdown

    • Presets

      • Yes

      • No

    • Default = Yes

    Criteria 1 - Operator

    Text

    • Default = >=

    Criteria 1 - Source Data Field

    Text

    • Default = Cq

    Criteria 1 - Threshold Value

    Numeric

    • Default = 7

    Criteria 2 - Operator

    Text

    • Default = <=

    Criteria 2 - Source Data Field

    Text

    • Default = Cq

    Criteria 2 - Threshold Value

    Numeric

    • Default = 25

    Instruction Notes

    Multiline Text

    Read Only

    • Default = 1. Set reaction volume and adding Rox? then click on calculate qPCR Master Mix and Sample Volume button. 2. Combine KAPA SYBR FAST qPCR Master Mix + Primer Premix, ROX and PCR-grade water to produce the qPCR Master Mix. 3. Add the qPCR Master Mix and Sample volume to a new 96 well PCR plate, seal the plate, vortex briefly to mix and then centrifuge. 4. Place the plate on the qPCR instrument. 5. Select Absolute Quantification and run the following cycling protocol: - Initial denaturation Temp. at 95C fro 5 mins for 1 cycle - Denaturation Temp. at 95C for 30 secs for 35 cycles - Annealing/Extension/Data acquisition Temp. at 95C for 45 sec for 35 cycles - Melt curve analysis (C) between 65C - 95C 6. Upload Cq values 7. Set Cq Thresholds then click on Assign QC Flags button. 8. Review Cq values and remove outliers. 9. Click on Calculate Average Cq.

    KAPA SYBR FAST qPCR Master Mix + Primer Premix (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 2

    PCR-grade water (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 2

    qPCR Master Mix with Primer Prep Date

    Date

    Reaction Volume (uL)

    Numeric Dropdown

    • Presets

      • 20

      • 10

    • Default = 20

    • Decimal Places Displayed = 0

    ROX (uL)

    Numeric

    Read Only

    • Decimal Places Displayed = 2

    Total Samples

    Numeric

    Read Only

    • Default = 0

  • Step File Placeholders

    • Log - Automatically attached

    • QC Log File - Automatically attached

    • QC Result File - Automatically attached

    • Upload File - Manually uploaded

  • 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

      Container

      Container Name

      Built-in

      Container

      LIMS ID (Container)

      Built-in

      Container

      Well

      Built-in

      Derived Sample

      Average Cq

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Cq

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Dilution Factor

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • 1:10000

      • 1:20000

      Derived Sample

      qPCR master mix (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Derived Sample

      Sample (uL)

      Numeric

      Decimal Places Displayed = 0

      Measurement

      Cq

      Numeric

      Decimal Places Displayed = 2

      Measurement

      qPCR master mix (uL)

      Numeric

      Measurement

      Sample (uL)

      Numeric

      Project

      Project Name

      Built-in

Step 3: KAPA Library Quantification (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = KAPA Library Quantification - Illumina/Universal v1.0

  • Step Type = Standard QC

  • Measurement Generation = Fixed, 1

  • Naming Convention = {InputItemName}

Automations

Calculate Library Length Ratio & Copy Dilution Factor and Average Cq
  • 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.::Library Length Ratio:: = 452 / step.::Library Length (bp):: ; \
output.::Average Cq:: = input.::Average Cq:: ; \
output.::Dilution Factor:: = input.::Dilution Factor::' \
-log {compoundOutputFileLuid0}"
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 -u {username} -p {password} \
      script:assignQC \
        -i {processURI:v2} \
        -log {compoundOutputFileLuid1} \
        -qcResult {compoundOutputFileLuid2}"
Calculate Concentration
  • 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.::Diluted Avg. Conc. (pM)::  = 10 ** ((output.::Average Cq:: - step.::Standard Curve Y-Intercept::) / step.::Standard Curve Slope::) ; \
if (output.::Dilution Factor::.toFloat() >= 1) {output.::Concentration (pM):: = output.::Diluted Avg. Conc. (pM):: * step.::Library Length Ratio:: * output.::Dilution Factor::.toFloat()} else {output.::Concentration (pM):: = output.::Diluted Avg. Conc. (pM):: * step.::Library Length Ratio::} ; \
output.::Concentration (nM):: = 0.001 * output.::Concentration (pM)::' \
-log {compoundOutputFileLuid0}"
Set Next Step-KAPA Lib Quant
  • 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 'if (output.name.contains(::KAPA::)) {nextStep = ::REMOVE::} else {nextStep = ::ADVANCE::} ; \
input.::Concentration (nM):: = output.::Concentration (nM)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • 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::' \
      -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

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Criteria 1 - Operator

    Text

    Default = >=

    Criteria 1 - Source Data Field

    Text

    Default = Concentration (nM)

    Criteria 1 - Threshold Value

    Numeric

    Default = 25

    Criteria 2 - Operator

    Text

    Default = <=

    Criteria 2 - Source Data Field

    Text

    Default = Concentration (nM)

    Criteria 2 - Threshold Value

    Numeric

    Default = 99

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Enter the Slope and the Y-Intercept for your standard curve then click on the Calculate Concentration button. 2. Set your Concentration Threshold then click on the Assign QC Flogs button.

    Library Length (bp)

    Numeric

    Default = 450

    Library Length Ratio

    Numeric

    Read Only

    Decimal Places Displayed = 0

    Standard Curve Slope

    Numeric

    Standard Curve Y-Intercept

    Numeric

  • Step File Placeholders

    • Log - Automatically attached

    • QC Log File - Automatically attached

    • QC Result File - Manually uploaded

    • Upload File - Manually uploaded

  • Sample Table

    • Enable QC Flags = Yes

    • Sample Display Default = Expand

    • Well Sort Order = Column

    • File Column Options

      • File Column Display = Show

      • File Attachment Method = Manual

    • 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

      Average Cq

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Concentration (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Concentration (pM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Diluted Avg. Conc. (pM)

      Numeric

      Derived Sample

      Dilution Factor

      Text Dropdown

      • Required Field

      • Custom Entries

      Presets

      • 1:10000

      • 1:20000

      Derived Sample

      Sample Name

      Built-in

      Measurement

      Average Cq

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Concentration (nM)

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Concentration (pM)

      Numeric

      Decimal Places Displayed = 2

      Measurement

      Diluted Avg. Conc. (pM)

      Numeric

      Decimal Places Displayed = 4

      Measurement

      Dilution Factor

      Text

      • Read Only

      Project

      Project Name

      Built-in

Step 4: Dilute Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Dilute Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Standard

  • Derived Sample Generation = Fixed, 1

  • Naming Convention = {InputItemName}

  • Reagent Kits

    • Resuspension Buffer (RSB)

Automations

Copy Concentration (nM)
  • 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 'output.::Concentration (nM):: = input.::Concentration (nM)::' \
-log {compoundOutputFileLuid0}"
Calculate Dilution Volumess
  • 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 false \
-h false \
-exp 'output.::Sample (uL):: = (step.::Final Concentration (nM):: * step.::Final Volume (uL)::) / output.::Concentration (nM):: ; \
output.::RSB (uL):: = step.::Final Volume (uL):: - output.::Sample (uL):: ; \
output.::Final Concentration (nM):: = step.::Final Concentration (nM)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Final Concentration (nM)

    Numeric

    Default = 2

    Final Volume (uL)

    Numeric

  • Step File Placeholders

    • Log - 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

      Concentration (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Final Concentration (nM)

      Numeric

      Derived Sample

      RSB (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample (uL)

      Numeric

      Decimal Places Displayed = 0

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

Step 5: Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Master Step Name = Pool Libraries - Low Input (Illumina DNA PCR-Free Library Prep Manual v1.0.3)

  • Step Type = Pooling

  • Aliquot Generation = Fixed, 1

  • Naming Convention = {PoolName}

Automations

Copy Final Concentration (nM)
  • 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 'output.::Concentration (nM):: = input.::Final Concentration (nM)::' \
-log {compoundOutputFileLuid0}"
Set Next Step - Advance
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

  • Sample Table (Column Headers)

    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

Pooling

  • Label Uniqueness = On

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Column

Record Details

  • Step Data (Master Step Fields)

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Instruction Notes

    Multiline Text

    Read Only

    Default = 1. Combine libraries equimolarly to a 2 nM final concentration. 2. Vortex to mix, and then centrifuge at 280 x g for 1 minute.

    Sample Volume (uL)

    Numeric

  • Step File Placeholders

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • 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

      Concentration (nM)

      Numeric

      Decimal Places Displayed = 2

      Derived Sample

      Sample Name

      Built-in

      Project

      Project Name

      Built-in

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