TruSeq ChIP-Seq v1.0

Protocol 1: TruSeq ChIP-Seq v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Normalize DNA (TruSeq ChIP-Seq v1.0)

• Master Step Name = Normalize DNA (TruSeq ChIP-Seq v1.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}

Automations

Normalization Calculations

• Trigger Location = Record Details
• Trigger Style = Manual button

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Final Volume (ul)	Numeric	Required Field	Default = 50 Decimal Places Displayed = 2
  Input Amount (pg/ul)	Numeric	Required Field	Range From 100 to 200 Decimal Places Displayed = 0

• Step File Placeholders

  • Log File - Automatically attached
• 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	Sample Name	Built-in
    Derived Sample	Sample Volume (ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: End Repair (TruSeq ChIP-Seq v1.0)

• Master Step Name = Repair Ends v1.0
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • AMPure XP Beads

    • Supplier = Beckman Coulter Genomics
    • Catalog Number = A63881
    • Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
  • TruSeq ChIP Sample Prep Kit, Box A or B

    • Supplier = Illumina
    • Catalog Number = 15034288; 15034289
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

SPB Dilution

• Trigger Location = Not Used

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

  • Next Step Log - Automatically attached
• 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	Sample Name	Built-in
    Project	Project Name	Built-in

Step 3: Adenylate 3' Ends (TruSeq ChIP-Seq v1.0)

• Master Step Name = Adenylate 3' Ends v2.0
• Step Type = No Outputs
• Reagent Kits

  • TruSeq ChIP Sample Prep Kit, Box A or B

    • Supplier = Illumina
    • Catalog Number = 15034288; 15034289
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  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
    Project	Project Name	Built-in

Step 4: Ligate Indexed Paired-End Adapters (TruSeq ChIP-Seq v1.0)

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

  • AMPure XP Beads

    • Supplier = Beckman Coulter Genomics
    • Catalog Number = A63881
    • Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
  • TruSeq ChIP Sample Prep Kit, Box A or B

    • Supplier = Illumina
    • Catalog Number = 15034288; 15034289
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Copy to Output

• Trigger Location = Not Used

Set Next Step & Copy to Input

• Trigger Location = Not Used

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

Add Labels

• Label Groups

  • TruSeq ChIP

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	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	Reagent Name	Built-in
    Derived Sample	Sample Name	Built-in
    Project	Project Name	Built-in

Step 5: Purify Ligation Products (TruSeq ChIP-Seq v1.0)

• Master Step Name = Purify Ligation Products (TruSeq ChIP-Seq v1.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • 6X gel loading dye

    • Supplier = BioLabs
    • Catalog Number = B7021S
  • 50 bp DNA ladder

    • Supplier = NEB
    • Catalog Number = N3236L
  • 50X TAE buffer

    • Supplier = Bio-Rad
    • Catalog Number = 161-0743
  • 100bp DNA ladder

    • Supplier = NEB
    • Catalog Number = N3231L
  • Certified low-range ultra agarose

    • Supplier = Bio-Rad
    • Catalog Number = 161-3107
  • MinElute Gel Extraction Kit

    • Supplier = QIAGEN, part # 28604
    • Catalog Number = 28604
  • SYBR Gold Nucleic acid gel stain

    • Supplier = Invitrogen
    • Catalog Number = S11494
  • TruSeq ChIP Sample Prep Kit, Box A or B

    • Supplier = Illumina
    • Catalog Number = 15034288; 15034289
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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

• Step File Placeholders

  • Log File - Automatically attached
  • Gel Image - 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	Sample Name	Built-in
    Project	Project Name	Built-in

Step 6: Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)

• Master Step Name = Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}
• Reagent Kits

  • AMPure XP Beads

    • Supplier = Beckman Coulter Genomics
    • Catalog Number = A63881
    • Website = https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm
  • TruSeq ChIP Sample Prep Kit, Box A or B

    • Supplier = Illumina
    • Catalog Number = 15034288; 15034289
    • Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html
  • TruSeq ChIP Sample Prep Kit, PCR Box

    • Supplier = Illumina
    • Catalog Number = 15027084

Automations

Set Next Step - Advance

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

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
  Number of PCR Cycles	Numeric		Default = 18 Decimal Places Displayed = 0
  Thermal Cycler Program	Text		Default = PCR
  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	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
    Project	Project Name	Built-in

Step 7: Bioanalyzer QC (Library Validation) (TruSeq ChIP-Seq v1.0)

• Master Step Name = Bioanalyzer QC (Library Validation) v2.0
• Step Type = Standard QC
• Measurement Generation = Fixed, 1
• Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input file

• Trigger Location = Record Details
• Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Copy nM and Assign QC flags

• Trigger Location = Record Details
• Trigger Style = Manual button

Set Next Step - Output PASS/FAIL

• Trigger Location = Record Details
• Trigger Style = Automatic upon exit

Parse Bioanalyzer XML and assign QC flags

• Trigger Location = Not Used

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

• Trigger Location = Not Used

Parse Bioanalyzer XML, Calculate nM and assign QC flags

• Trigger Location = Not Used

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	LIMS ID (Container)	Built-in
  Container	Well	Built-in
  Derived Sample	Sample Name	Built-in
  Derived Sample	Waiting	Built-in
  Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Containers
  • Well Sort Order = Column
  • Placement Pattern = Column
• Destination Containers

  • BioAnalyzer DNA High Sensitivity Chip

  

  • BioAnalyzer DNA 1000 Chip

  

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

• Criteria 1 - Operator = >=
• Criteria 1 - Source Data Field = Peak 2 Size - bp
• Criteria 1 - Threshold Value = 150.00
• Criteria 2 - Operator = <=