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TruSeq Methyl Capture EPIC v2.0

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

Last updated 16 days 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
  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

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)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Control Concentration (ng/ul)
Numeric
Required Field
Default = 0
Decimal Places Displayed = 2
Control Type
Text Dropdown
Custom Entries
Presets
HCC1187 normal (BL) (ATCC, catalog # CRL2323-D)
NA12878 (Coriell Institute, catalog # NA12878)
HCC1187 breast cancer tumor (ATCC, catalog # CRL2322)
HeLa (Biochain, catalog # D1255811)
Jurkat (Biochain, catalog # D1255815)
Cycles/Burst
Numeric
Default = 200
Decimal Places Displayed = 0
Duration (seconds)
Numeric
Default = 280
Decimal Places Displayed = 0
Duty Factor (%)
Numeric
Default = 10
Decimal Places Displayed = 0
Peak/Displayed Power (W)
Numeric
Default = 175
Decimal Places Displayed = 0
RSB (mL)
Numeric
Decimal Places Displayed = 2
Temperature (C)
Numeric
Default = 7
Decimal Places Displayed = 0
Total Samples
Numeric
Default = 0
Water Level
Numeric
Default = 12
Decimal Places Displayed = 0
0.5 EDTA (uL)
Numeric
Decimal Places Displayed = 2
Step File Placeholders
- Log File - Manually uploaded
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Container
  Container Name
  Built-in
  Container
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Buffer Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Derived Sample
  Concentration
  Numeric
  Required Field
  Decimal Places Displayed = 2
  Derived Sample
  Conc. Units
  Numeric
  Required Field
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Sample Volume (ul)
  Numeric
  Decimal Places Displayed = 2
  Project
  Project Name
  Built-in

Step 2: 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 \