TruSeq Methyl Capture EPIC v2.0
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
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
Parse Bioanalyzer XML and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
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 = 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
Field Name
Field Type
Options
Additional Options and Dropdown Items
Criteria 1 - Operator
Text Dropdown
Presets
>=
<=
=
!=
Criteria 1 - Source Data Field
Text Dropdown
Presets
Concentration
Conc. Units
Number of Peaks found
Peak 1 Size - bp
Peak 1 Conc.
Peak 1 Molarity
Peak 2 Size - bp
Peak 2 Conc.
Peak 2 Molarity
Peak 3 Size - bp
Peak 3 Conc.
Peak 3 Molarity
Peak 4 Size - bp
Peak 4 Conc.
Peak 4 Molarity
Peak 5 Size - bp
Peak 5 Conc.
Peak 5 Molarity
Number of Regions found
Region 1 Average Size - bp
Region 1 Conc.
Region 1 Molarity
Region 2 Average Size - bp
Region 2 Conc.
Region 2 Molarity
Region 3 Average Size - bp
Region 3 Conc.
Region 3 Molarity
Region 4 Average Size - bp
Region 4 Conc.
Region 4 Molarity
Region 5 Average Size - bp
Region 5 Conc.
Region 5 Molarity
Criteria 1 - Threshold Value
Numeric
Decimal Places Displayed = 2
Criteria 2 - Operator
Text Dropdown
Presets
>=
<=
=
!=
Criteria 2 - Source Data Field
Text Dropdown
Presets
Concentration
Conc. Units
Number of Peaks found
Peak 1 Size - bp
Peak 1 Conc.
Peak 1 Molarity
Peak 2 Size - bp
Peak 2 Conc.
Peak 2 Molarity
Peak 3 Size - bp
Peak 3 Conc.
Peak 3 Molarity
Peak 4 Size - bp
Peak 4 Conc.
Peak 4 Molarity
Peak 5 Size - bp
Peak 5 Conc.
Peak 5 Molarity
Number of Regions found
Region 1 Average Size - bp
Region 1 Conc.
Region 1 Molarity
Region 2 Average Size - bp
Region 2 Conc.
Region 2 Molarity
Region 3 Average Size - bp
Region 3 Conc.
Region 3 Molarity
Region 4 Average Size - bp
Region 4 Conc.
Region 4 Molarity
Region 5 Average Size - bp
Region 5 Conc.
Region 5 Molarity
Criteria 2 - Threshold Value
Numeric
Decimal Places Displayed = 2
Use strict matching for Bioanalyzer results
Toggle Switch
Default = None Set
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
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
Measurement
A260/280 ratio
Numeric
Decimal Places Displayed = 2
Measurement
BA Sample Name
Text
Measurement
Concentration
Numeric
Decimal Places Displayed = 2
Measurement
Conc. Units
Text
Measurement
Number of Peaks found
Numeric
Decimal Places Displayed = 0
Measurement
Number of Regions found
Numeric
Decimal Places Displayed = 0
Measurement
Peak 1 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Peak 1 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Peak 1 Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Peak 2 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Peak 2 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Peak 2 Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Peak 3 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Peak 3 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Peak 3 Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Peak 4 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Peak 4 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Peak 4 Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Peak 5 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Peak 5 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Peak 5 Size - bp
Numeric
Decimal Places Displayed = 2
Measurement
Region 1 Average Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Region 1 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Region 1 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Region 2 Average Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Region 2 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Region 2 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Region 3 Average Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Region 3 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Region 3 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Region 4 Average Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Region 4 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Region 4 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Region 5 Average Size - bp
Numeric
Decimal Places Displayed = 0
Measurement
Region 5 Conc.
Numeric
Decimal Places Displayed = 2
Measurement
Region 5 Molarity
Numeric
Decimal Places Displayed = 2
Measurement
Sample Comment
Text
Project
Project Name
Built-in
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
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
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
80% EtOH Prep Date
Date
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Category
Field Name