AmpliSeq for Illumina Transcriptome Human Gene Expression Panel

The AmpliSeq for Illumina Transcriptome Human Gene Expression Panel includes the following functionality:

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Preconfigured AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of total RNA using the AmpliSeq for Illumina workflow.

•

Automated calculation of sample and buffer volumes. Automated calculation or display of reagents at every step in the protocol.

•

Automatic step transition when required.

•

Automatic placement of samples when necessary.

•

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

•

There is no extraction protocol in this workflow because the samples are already extracted.

Master Step 1: Dilute RNA (AmpliSeq for Illumina v1.0)

Step Type: Standard

Input = RNA with concentration

Output = Diluted RNA (1-100 ng)

Placement

•

Master Step

•

None

•

Step

•

Tube

Record Details

•

Step Data

•

Master Step Fields

•

Desired Concentration (ng/uL)

•

Numeric

–

Range 20 - 50

•

Multiline Text Fields

•

Directions

•

Multi-line text

–

Preset = If enough DNA is available, dilute to intermediate concentration ~20-50 ng/uL.

–

Read only

•

Step File Placeholders

•

Log

•

Auto

•

Table Columns

•

Concentration

•

Numeric

–

Conc. Units

–

Single-line text

–

Input Amount (ng)

–

Numeric

–

Nuclease-free water (uL)

–

Numeric

–

Sample Volume (uL)

–

Numeric

–

Total Volume (uL)

–

Numeric

Automation - Script description

•

Copy Concentration and Set Sample Volume

•

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 Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]

•

Calculate Input Amount

•

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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]

•

Copy Desired Concentration

•

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 -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'output.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]

[Optional] Next Steps:

•

Qubit (AmpliSeq for Illumina Immune Response Panel v1.0)

•

Reverse Transcribe RNA (AmpliSeq for Illumina Immune Response Panel v1.0)

Start Next Step - manual

Assign Next Step - Manual

Must move forward.

Master Step 2: Qubit (AmpliSeq for Illumina v1.0)

Step Type: Standard QC

Input = Diluted RNA (1-100 ng)

Output = Measurement

Placement

•

Master Step

•

None

•

Step

•

Tube

Record Details

•

Step Data

•

Master Step Fields

•

Criteria 1 - Source Data Field

•

Text

–

Preset = Concentration

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Criteria 1 - Operator

–

Text

–

Preset: >=

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Criteria 1 - Threshold Value

–

Numeric

–

Criteria 2 - Source Data Field

–

Text

–

Preset = Concentration

–

Criteria 2 - Operator

–

Text

–

Preset: <=

–

Criteria 2 - Threshold Value

–

Numeric

•

Step File Placeholders

•

Log

•

Auto

–

QC Log File

–

Auto

–

QC Result File

–

Manual

–

Upload File

–

Manual

•

Table Columns

•

Concentration

•

Derived Sample

–

Numeric

–

Conc. Units

–

Derived Sample

–

Text

Automation - Script description

•

Assign QC Flags

•

Trigger location: Record Details

–

Trigger Style: Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"

–

Set Next Step 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 = ::ADVANCE:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"

Start Next Step - Automatic

Assign Next Step - Automatic

Must move forward.

Master Step 3: Dilute RNA (AmpliSeq for Illumina v1.0)

Step Type:

Input = Diluted RNA with concentration

Output = Diluted RNA (1-100 ng)

Place Samples = Tube

Record Details =

•

PlaceholderLog

•

Step UDF Desired Concentration (ng/uL)

•

Range 20 - 50

•

Analyte UDF = Concentration

•

Numeric

–

Conc. Units

–

Single-line text

–

Input Amount (ng)

–

Numeric

–

Nuclease-free water (uL)

–

Numeric

–

Sample Volume (uL)

–

Numeric

–

Total Volume (uL)

–

Numeric

•

Script description

•

Copy Concentration and Set Sample Volume

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 Volume (uL):: = 5' \-log {compoundOutputFileLuid0}["]

–

Calculate Input Amount

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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Sample Volume (uL):: ' \-log {compoundOutputFileLuid0}["]

–

Set Next Step - Advance and Set Desired Conc

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'nextStep = ::ADVANCE:: ; output.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]

–

Copy Desired Concentration

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 Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]

Next Steps:

Reverse Transcribe RNA (AmpliSeq for Illumina Immune Response Panel v1.0)

•

Automatic Transition

Master Step 4: Reverse Transcribe RNA (AmpliSeq for Illumina v1.0)

Input = RNA with concentration

Output = Reverse Transcribed RNA

Place Samples = 96 well plate

Reagent Kits =

•

AmpliSeq cDNA Synthesis for Illumina

•

Supplier - Illumina

–

Cat. # - 20022654

–

Website - www.illumina.com

Record Details =

•

Placeholder

•

Log

•

Step UDF Directions (multi-line text)

•

If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.

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AmplISeq ERCC RNA Spike-in Mix (toggle)

–

AmpliSeq ERCC RNA Spike-in Mix for Illumina (uL) (Number - 2 decimal places, range = 0-2, default = 0)

–

AmpliSeq ERCC RNA Spike-in Mix for Illumina Lot# (Text)

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Thermal Cycler Program

–

Preset = RT

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5X AmpliSeq cDNA Reaction Mix (uL)

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10X AmpliSeq RT Enzyme Mix (uL)

–

Nuclease-free water (uL)

–

Prep Input Volume (uL)

–

Calculated

–

Numeric

–

Prep Input Amount (ng)

–

User input

–

Mandatory

–

Range - 1-100

–

Total Samples

Analyte UDF = Concentration

–

Conc. Units

–

Total Volume (uL)

–

Numeric

–

Input Amount (ng)

–

AmpliSeq ERCC RNA Spike-in Volume (uL)

•

Script description

•

Copy Concentration, Total Volume and Input Amount

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \script:evaluateDynamicExpression \-t false \-h false \-exp 'output.::Concentration:: = input.::Concentration:: ; \output.::Conc. Units:: = input.::Conc. Units:: ; \output.::Total Volume (uL):: = input.::Total Volume (uL):: ; \output.::Input Amount (ng):: = input.::Input Amount (ng):: ; \step.::Desired Concentration (ng/uL):: = input.::Desired Concentration (ng/uL)::' \-log {compoundOutputFileLuid0}["]

–

Calculate Input Amount -  Transcriptome Human Genome Expression Panel

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.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \if (step.::Prep Input Volume (uL):: < 7.0) {step.::Nuclease-free water (uL):: = (7.0 - (step.::Prep Input Volume (uL):: + output.::AmpliSeq ERCC RNA Spike-in Volume (uL)::)) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5 ; \step.::AmpliSeq ERCC RNA Spike-in Mix (uL):: = step.::Total Samples:: * output.::AmpliSeq ERCC RNA Spike-in Volume (uL):: *1.1' \-log {compoundOutputFileLuid0}["]

–

Set Next Step - Advance

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}["]

•

Automatic Transition

Master Step 5: Amplify cDNA Targets Standard (AmpliSeq for Illumina v1.0) >> New Master Step with with no reps = variable output = 1.

Input = Reverse Transcribed RNA

Output = cDNA

Place Samples = 96 well plate

Variable Outputs = 1

Sample Name = {InputItemName}_{OutputItemSubsetNumber}

Reagent Kits =

•

AmpliSeq Library PLUS for Illumina

•

Supplier - Illumina

–

Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103

–

Website - www.illumina.com

•

AmpliSeq Transcriptome Gene Expression Panel for Illumina

•

Supplier - Illumina

–

Cat. # - 20019170

–

Website - www.illumina.com

Record Details =

•

PlaceholderLog

•

Step UDF Thermal Cycler ProgramPreset = AMP_RNA

–

AmpliSeq ERCC RNA Companion Panel for Illumina (toggle)

–

AmpliSeq ERCC RNA Companion Panel for Illumina Lot# (text)

–

5X AmpliSeq HiFi Mix (uL)

–

Decimal Places = 2

–

Nuclease-free water (uL)

–

Decimal Places = 2

–

PCR Cycles

Analyte UDF = None

•

Script description

Set Sample Type and Calculate Master Mix - TGx Panel

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \script:evaluateDynamicExpression \-t false \-h false \-exp 'output.::Sample Type:: = ::cDNA:: ; \step.::5X AmpliSeq HiFi Mix (uL):: = 4 * step.::Total Samples:: * 1.1 ; \step.::Nuclease-free water (uL):: = 3 * step.::Total Samples:: * 1.1' \-log {compoundOutputFileLuid0}["]

–

Set Next Step - Advance

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}["]

Master Step 6: Partially Digested Amplicons (AmpliSeq for Illumina v1.0)

Input = Pooled samples

Output = Partially Digested Amplicons

No Output

Reagent Kits =

•

AmpliSeq Library PLUS for Illumina

•

Supplier - Illumina

–

Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103

–

Website - www.illumina.com

Record Details =

•

Placeholder

•

Log

•

Step UDF Thermal Cycler Program

•

Preset FUPA

•

Script description

•

Set Next Step - Advance

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}["]

Safe Stopping Point

Master Step 7: Ligate Indexes (AmpliSeq for Illumina v1.0)

Input = Partially Digested Amplicons

Output = Ligated Libraries

Place Samples = 96 well plate

Add Labels

Reagent Kits =

•

AmpliSeq Library PLUS for Illumina

•

Supplier - Illumina

–

Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103

–

Website - www.illumina.com

Index List (5.x)

•

AmpliSeq CD Indexes Set A for Illumina - AmpliSeq CD Indexes Set A for Illumina-label-sheet.xlsx

•

AmpliSeq CD Indexes Set B for Illumina - AmpliSeq CD Indexes Set B for Illumina-label-sheet.xlsx

•

AmpliSeq CD Indexes Set C for Illumina - AmpliSeq CD Indexes Set C for Illumina-label-sheet.xlsx

•

AmpliSeq CD Indexes Set D for Illumina - AmpliSeq CD Indexes Set D for Illumina-label-sheet.xlsx

•

AmpliSeq UD Indexes for Illumina (24 Indexes) - AmpliSeq UD Indexes for Illumina (24 Indexes)-label-sheet.xlsx

Record Details =

•

Placeholder

•

Log File

•

Step UDF

•

Thermal Cycler Program

•

Preset LIGATE

•

Analyte UDF AmpliSeq Workflow Presets

•

Standard Workflow or Equalizer Workflow

–

Mandatory

Script description

Set Next Step - Advance

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}["]

Route AmpliSeq Samples -Transcriptome Human GEx Panel

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 'AmpliSeq Workflow' \--FIELD_VALUE 'Standard Workflow' \--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.0' \--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME 'AmpliSeq Workflow' \--FIELD_VALUE 'Equalizer Workflow' \--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.0' \--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS'["]

Safe Stopping Point

Master Step 1: Clean Up Library (AmpliSeq for Illumina v1.0)

Input = Ligated Libraries

Output = Cleaned Up Libraries

No Output

Reagent Kits =

•

Agencourt AMPure XP Beads

•

Supplier - Thermo

–

Cat. # - NC9959336; NC9933872

Record Details =

•

Placeholder

•

Log File

•

Step UDF

•

70% EtOH Prep Date

•

Date

•

Script description

•

Set Next Step - Advance

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}["]

Automatic Transition

Master Step 2: Amplify Library (AmpliSeq for Illumina v1.0)

Input = Cleaned Up Libraries

Output = Amplified Libraries

No Output

Reagent Kits =

•

Agencourt AMPure XP Beads

•

Supplier - Thermo

–

Cat. # - NC9959336; NC9933872

•

AmpliSeq Library PLUS for Illumina

•

Supplier - Illumina

–

Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103

–

Website - www.illumina.com

Record Details =

•

Placeholder

•

Log

•

Step UDF

•

Thermal Cycler Program

–

Total Samples

–

Preset 0

–

1X Lib AMP Mix (uL)

–

Numeric

–

10X Library Amp Primers (uL)

–

Numeric

–

Group of Defaults Standard Workflow = AMP_7

•

Script description Calculate Total Samples and Calculate Master Mix

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \-log {compoundOutputFileLuid0}["]

–

Set Next Step - Advance

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}["]

Safe Stopping Point

Master Step 3: Perform Second Clean Up (AmpliSeq for Illumina BRCA Panel v1.0)

Input = Amplified Libraries

Output = Cleaned Up Amplified Libraries

Place Samples = 96 well plate

Reagent Kits =

•

Agencourt AMPure XP BeadsSupplier - Thermo

–

Cat. # - NC9959336; NC9933872

•

AmpliSeq Library PLUS for IlluminaSupplier - Illumina

–

Cat. # - 24 - 20019101; 96 - 200191102; 384 - 200191103

–

Website - www.illumina.com

Record Details =

•

Placeholder

•

Log

•

Step UDF

•

70% EtOH Prep Date

•

Date

•

Script description

•

Set Next Step - Advance

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}["]

Master Step 1: Clean Up Library (AmpliSeq for Illumina v1.0)

Input = Ligated Libraries

Output = Cleaned Up Libraries

No Output

Reagent Kits =

•

Agencourt AMPure XP Beads

•

Supplier - Thermo

–

Cat. # - NC9959336; NC9933872

Record Details =

•

Placeholder

•

Log

•

Step UDF 70% EtOH Prep Date

•

Date

•

Script description

•

Set Next Step - Advance

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}["]

Automatic Transition

Master Step 2: Amplify Library (AmpliSeq for Illumina v1.0)

Input = Cleaned Up Libraries

Output = Amplified Libraries

No Output

Reagent Kits =

•

Agencourt AMPure XP Beads

•

AmpliSeq Library PLUS for Illumina

Record Details =

•

Placeholder

•

Log

•

Step UDF

•

Thermal Cycler Program

–

Total Samples

–

Preset 0

–

1X Lib AMP Mix (uL)

–

Numeric

–

10X Library Amp Primers (uL)

–

Numeric

•

Group of Defaults = Equalizer Workflow

•

Thermal Cycler Program = EQUAL

Script description Calculate Total Samples and Calculate Master Mix

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \script:evaluateDynamicExpression \-t false \-h false \-exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \-log {compoundOutputFileLuid0}["]

–

Set Next Step - Advance

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}["]

•

Automatic Transition

Master Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina v1.0)

Input = Amplified Libraries

Output = Cleaned Up Libraries

Place Samples = 96 well plate

Reagent Kits =

•

AmpliSeq Library Equalizer for Illumina

•

Supplier = Illumina

–

Cat. # =

–

Website = www.illumina.com

Record Details =

•

Placeholder

•

Log

Script description

Set Next Step - Advance

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}["]

Automatic Transition

Master Step 4: Elute Library (AmpliSeq for Illumina v1.0)

Input = Cleaned Up Libraries

Output = Final Library

Place Samples = 96 well plate

Reagent Kits =

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AmpliSeq Library Equalizer for Illumina

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Supplier = Illumina

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Cat. # =

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Website = www.illumina.com

Record Details =

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Placeholder

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Log

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Step UDF

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Thermal Cycler Program

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Present ELUTE

Script description

Set Next Step - Advance

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}["]