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TruSeq DNA PCR-Free v2.0

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Last updated 16 days ago

Protocol 1: TruSeq DNA PCR-Free v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment DNA (TruSeq DNA PCR-Free v2.0)

Master Step Name = Fragment DNA v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box
  - Supplier = Illumina
  - Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

Normalize gDNA (PCR Free)

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 'if ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 1000 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 2000 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 55 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -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}"

Normalize gDNA (Nano)

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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if ( step.::Target Insert Size (bp):: == 350 ) { output.::Sample Volume (ul):: = 100 / output.::Concentration:: } ; if ( step.::Target Insert Size (bp):: == 550 ) { output.::Sample Volume (ul):: = 200 / output.::Concentration:: } ; output.::RSB Volume (ul):: = 52.5 - output.::Sample Volume (ul):: ; output.::Target Insert Size (bp):: = step.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Cycles/Burst
Numeric Dropdown
Custom Entries
Presets
200
Duration (seconds)
Numeric Dropdown
Custom Entries
Presets
65
50
45
25
Decimal Places Displayed = 0
Duty Factor (%)
Numeric Dropdown
Custom Entries
Presets
20
5
10
Decimal Places Displayed = 0
Intensity
Numeric Dropdown
Custom Entries
Presets
5
2
Decimal Places Displayed = 1
Mode
Text Dropdown
Custom Entries
Presets
Frequency sweeping
-
Peak/Displayed Power (W)
Numeric Dropdown
Custom Entries
Presets
50
175
23
14
9
7
Decimal Places Displayed = 0
Target Insert Size (bp)
Numeric Dropdown
Required Field
Custom Entries
Presets
350
550
Decimal Places Displayed = 0
Temperature (oC)
Numeric Dropdown
Custom Entries
Presets
20
6
80% EtOH Prep Date
Date
Step File Placeholders
- Log file - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Text
  Required Field
  Derived Sample
  RSB Volume (ul)
  Numeric
  Read Only
  Decimal Places Displayed = 2
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (uL)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

Step 2: Repair Ends and Select Library Size (TruSeq DNA PCR-Free v2.0)

Master Step Name = Repair Ends v1.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box
  - Supplier = Illumina
  - Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

SPB Dilution

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 Number of Samples:: = step.::Total Number of Samples:: + 1' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if(input.::Target Insert Size (bp):: == 350) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 109.25) / 1000} ; if(input.::Target Insert Size (bp):: == 350) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 74.75) / 1000 } ; if(input.::Target Insert Size (bp):: == 550) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 92) / 1000} ; if(input.::Target Insert Size (bp):: == 550) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 92) / 1000 } ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
SPB (ml)
Numeric
Decimal Places Displayed = 2
PCR Grade Water (ml)
Numeric
Decimal Places Displayed = 2
Thermal Cycler Program
Text
Default = ERP
Step File Placeholders
- Next Step 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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

Step 3: Adenylate 3' Ends (TruSeq DNA PCR-Free v2.0)

Master Step Name = Adenylate 3' Ends v2.0
Step Type = No Outputs
Reagent Kits
- TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box
  - Supplier = Illumina
  - Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Thermal Cycler Program
Text
Default = ATAIL70
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Column
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Project
  Project Name
  Built-in

Step 4: Ligate Adapters (TruSeq DNA PCR-Free v2.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq DNA PCR-Free Sample Prep Kit - Set A, B or HT Box
  - Supplier = Illumina
  - Catalog Number = Set A: FC-121-3001, Set B: FC-121-3002, HT: FC-121-3003

Automations

Copy to Output

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.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

Set Next Step & Copy to Input

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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Target Insert Size (bp)
  Numeric Dropdown
  Custom Entries
  Presets
  350
  550
  Decimal Places Displayed = 0
  Derived Sample
  Waiting
  Built-in
- Expanded View Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  LIMS ID (Container)
  Built-in
  Project
  Project Name
  Built-in

Add Labels

Label Groups
- TruSeq DNA HT
- TruSeq DNA LT