TruSight Oncology 500 v1.1

Protocol 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: DNA/RNA FFPE Extraction (TruSight Oncology 500 v1.1)

• Master Step Name = DNA/RNA FFPE Extraction (TSO 500 HT v1.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 2
• Naming Convention = {LIST:{SubmittedSampleName}_DNA,{SubmittedSampleName}_RNA}
• Reagent Kits

  • QIAGEN AllPrep DNA/RNA FFPE Kit

    • Supplier = Qiagen
    • Catalog Number = 80234

The version of DNA/RNA FFPE Extraction master step name may be different depending on the version of IPP installed.

Automations

Set Sample Type

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

Set Next Step - Remove

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

Route DNA/RNA samples

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Route DNA/RNA samples - HT

• Trigger Location = Not Used

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

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

• 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	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Project	Project Name	Built-in

Protocol 2: RNA QC and cDNA Synthesis (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit RNA QC (TruSight Oncology 500 v1.1)

• Master Step Name = Qubit RNA QC (TSO 500 v1.1)
• Step Type = Standard QC
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}

The version of Qubit RNA QC master step name may be different depending on the version of IPP installed.

Automations

Assign QC flags - RNA

• 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 = 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	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    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
  Criteria 1 - Operator	Text Dropdown	Custom Entries	Presets >= <= = != Default = >=
  Criteria 1 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 1 - Threshold Value	Numeric		Default = 4.7 Decimal Places Displayed = 2
  Criteria 2 - Operator	Text Dropdown	Custom Entries	Presets >= <= = != Default = >=
  Criteria 2 - Source Data Field	Text		Default = Concentration (ng/ul)
  Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2

• Step File Placeholders

  • Log File - Automatically attached
  • Qubit Result File - Manually uploaded
• Sample Table

  • Enable QC Flags = Yes
  • Sample Display Default = Expand
  • Well Sort Order = Column
  • 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	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Derived Sample	Sample Name	Built-in
    Measurement	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    Project	Project Name	Built-in

Step 2: Denature and Anneal RNA (TruSight Oncology 500 v1.1)

• Master Step Name = Denature and Anneal RNA (TSO 500 v1.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {InputItemName}

The version of Denature and Anneal RNA master step name may be different depending on the version of IPP installed.

Automations

Count Samples and Calculate Master Mix

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

RNA Sample Dilution

• 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 = 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	Concentration (ng/ul)	Numeric		Decimal Places Displayed = 2
    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
  Dilution Concentration (ng/ul)	Numeric	Required Field	Range = 4.7 To 10 Decimal Places Displayed = 1
  EPH3 to each well (uL)	Numeric		Default = 8.5
  FSM (uL)	Text
  RVT (uL)	Text
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets LQ-RNA HQ-RNA
  Total Samples	Numeric		Default = 0

• Step File Placeholders

  • Calculation Log File - Automatically attached
  • NextStep 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	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 3: First Strand cDNA Synthesis (TruSight Oncology 500 v1.1)

• Master Step Name = First Strand cDNA Synthesis v2.0
• Step Type = No Outputs

The version of First Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.

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 = 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
  Thermal Cycler Program	Text Dropdown	Custom Entries	Presets Synthesize 1st Strand 1stSS

• Step File Placeholders

  • Log File - Automatically attached
• Sample Table

  • Sample Display Default = Collapse
  • 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: Second Strand cDNA Synthesis (TruSight Oncology 500 v1.1)

• Master Step Name = Second Strand cDNA Synthesis (TruSight Oncology 500 HT v1.1)
• Step Type = No Outputs
• Reagent Kits

  • TruSight Oncology 500, Box 1

    • Supplier = Illumina
    • Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
    • Website = www.illumina.com

The version of Second Strand cDNA Synthesis master step name may be different depending on the version of IPP installed.

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 = 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
  Thermal Cycler Program	Text	Read Only	Default = 2ndSS

• Step File Placeholders

  • Log File - Automatically attached
• Sample Table

  • Sample Display Default = Collapse
  • 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 5: cDNA Clean Up (TruSight Oncology 500 v1.1)

• Master Step Name = cDNA Clean Up (TSO 500 v1.1)
• Step Type = Standard
• Derived Sample Generation = Fixed, 1
• Naming Convention = {SubmittedSampleName}_cDNA
• Reagent Kits

  • TruSight Oncology 500, Box 4

    • Supplier = Illumina
    • Catalog Number = 20028213, 20028215, 20028215, 20028216, 20032624, 20032626, 20032625, 20032627
    • Website = www.illumina.com

The version of cDNA Clean Up master step name may be different depending on the version of IPP installed.

Automations

Assign Sample Type

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

Set Next Step - Remove

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

Routing cDNA Samples

• Trigger Location = Step
• Trigger Style = Automatic upon exit

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

Routing cDNA Samples - HT

• Trigger Location = Not Used

ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

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
  BIND1 Plate Barcode	Text
  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	Sample Name	Built-in
    Derived Sample	Sample Type	Text Dropdown	Required Field Custom Entries	Presets DNA RNA
    Project	Project Name	Built-in

Protocol 3: DNA QC and Fragmentation (TruSight Oncology 500 v1.1)

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Qubit DNA QC (TruSight Oncology 500 v1.1)

• Master Step Name = Qubit DNA QC (TruSight Oncology 500 HT v1.1)