TruSeq Methyl Capture EPIC v2.0

PreviousTruSeq DNA PCR-Free v2.0 NextTruSeq Nano DNA v1.0

Last updated 1 month ago

Protocol 1: TruSeq Methyl Capture EPIC v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Fragment DNA (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Fragment DNA (TruSeq Methyl Capture EPIC v2.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
Control Types
- HCC1187 breast cancer tumor (TruSeq Methyl EPIC v1.0)
  - Supplier = ATCC
  - Catalog Number = CRL2322
- HCC1187 normal (BL) (TruSeq Methyl EPIC v1.0)
  - Supplier = ATCC
  - Catalog Number = CRL2322-D
  - Conc. = 20
- Jurkat (TruSeq Methyl EPIC v1.0)
  - Supplier = Biochain
  - Catalog Number = D1255815
- NA12878 (TruSeq Methyl EPIC v1.0)
  - Supplier = Coriell Institute
  - Catalog Number = NA12878

Automations

Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total Samples:: = step.::Total Samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::RSB (mL):: = step.::Total Samples:: * 5 * 1.1 ; step.::0.5 M EDTA (uL):: = step.::Total Samples:: * 10 * 1.1 ; if (!input.name.contains(::TruSeq Methyl EPIC v1.0::)) {output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' -log {compoundOutputFileLuid1}"

Normalize gDNA

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 (input.name.contains( ::(TruSeq Methyl EPIC v1.0)::) ) { output.::Concentration:: = step.::Control Concentration (ng/ul):: ; output.::Conc. Units:: = ::ng/uL:: ; output.::Sample Volume (ul):: = 500 / step.::Control Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul):: } else {output.::Sample Volume (ul):: = 500 / input.::Concentration:: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul)::}' -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 1x8 Strip Tube

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 2: Bioanalyzer QC (DNA) (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Bioanalyzer QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer driver file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Record Details
Trigger Style = Manual button

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

Set Next Step - 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 true \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Set Next Step - Output PASS/FAIL

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

Set Next Step and Copy to Input

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Column
Destination Containers
- BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

NRCC

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Use strict matching for Bioanalyzer results = No

Peak 2 Size Thresholds

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Use strict matching for Bioanalyzer results = No

TruSeq ChIP-Seq

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Molarity
Criteria 1 - Threshold Value = 5.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Molarity
Criteria 2 - Threshold Value = 10.00
Use strict matching for Bioanalyzer results = No

TruSeq Methyl Capture EPIC

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00
Use strict matching for Bioanalyzer results = No

Step Data
- Group of Defaults = TruSeq Methyl Capture EPIC
- Master Step Fields
Step File Placeholders
- Bioanalyzer Driver File - Automatically attached
- Bioanalyzer Driver File Generation Log File - Automatically attached
- Bioanalyzer XML Result File (required) - Manually uploaded
- Result File (optional) - Manually uploaded
- PDF Summary File (optional) - Manually uploaded
- Bioanalyzer XML Parsing Log File - Automatically attached
- QC Assignment Log File - Automatically attached
- QC Assignment Report - Automatically attached
Sample Table
- Enable QC Flags = Yes
- Sample Display Default = Expand
- Well Sort Order = Row
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 3: Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0)
Step Type = No Outputs
Reagent Kits
- TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Repair Ends (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Repair Ends (TruSeq Methyl Capture EPIC v2.0)
Step Type = No Outputs
Reagent Kits
- TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 5: Adenylate 3' Ends (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Adenylate 3' Ends v2.0
Step Type = No Outputs
Reagent Kits
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Ligate Adapters (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Copy to Output

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"

Set Next Step and Copy to Input

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
Sample Table
- Column Headers
- Expanded View Fields

Add Labels

Label Groups
- TruSeq Methyl Capture EPIC

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Column
- Table Columns - Global Fields

Step 7: Clean Up and Pool Ligated Fragments (TruSeq Methyl Capture EPIC v2.0)

Master Step Name = Clean Up and Pool v2.0
Step Type = Pooling
Aliquot Generation = Fixed, 1
Naming Convention = {PoolName}
Reagent Kits
- TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com
- TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents
  - Supplier = Illumina
  - Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003
  - Website = https://support.illumina.com

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Protocol 1: TruSeq Methyl Capture EPIC v2.0

Step 1: Fragment DNA (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 2: Bioanalyzer QC (DNA) (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 3: Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 4: Repair Ends (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 5: Adenylate 3' Ends (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 6: Ligate Adapters (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Add Labels

Record Details

Step 7: Clean Up and Pool Ligated Fragments (TruSeq Methyl Capture EPIC v2.0)

Automations

Queue/Ice Bucket

Pooling