TruSeq RNA Access v2.0

Overview

The TruSeq RNA Access v2.0 workflow includes the following functionality:

Preconfigured TruSeq RNA Access v2.0 protocol that supports the conversion of total RNA or FFPE samples into a library of template molecules suitable for subsequent cluster generation and sequencing.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the workflow.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated generation of Bioanalyzer input file that the user may upload to the Bioanalyzer instrument’s Expert Software and use to set up a run.
Automated parsing of a Bioanalyzer instrument's XML result file into the LIMS, and storing of QC measurement records for the completed run.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Routing script that allows sequencing of libraries using any Illumina sequencing instrument.

Protocol 1: TruSeq RNA Access v2.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Sort Samples (TruSeq RNA Access v2.0)

Master Step Name = Sort Samples (TruSeq RNA Access v2.0.10)
Step Type = No Outputs

The version of Sort Samples master step name may be different depending on the version of IPP installed.

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Step 2: Fragment RNA (TruSeq RNA Access v2.0)

Master Step Name = Fragment RNA v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}

Automations

Dilute Total 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 = Row

Placement

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Step 3: First Strand cDNA Synthesis (TruSeq RNA Access v2.0)

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

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

Record Details

Step Data (Master Step Fields)

Step 4: Second Strand cDNA Synthesis (TruSeq RNA Access v2.0)

Master Step Name = Second Strand cDNA Synthesis v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1

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

Record Details

Step Data (Master Step Fields)

Step 5: Adenylate 3' Ends (TruSeq RNA Access v2.0)

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

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

Record Details

Step Data (Master Step Fields)

Step 6: Ligate Adapters (TruSeq RNA Access v2.0)

Master Step Name = Ligate Adapters v2.0
Step Type = Add Labels
Derived Sample Generation = Fixed, 1

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Manual button

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

Add Labels

Label Groups
- TruSeq RNA Access

Record Details

Step Data (Master Step Fields)

Step 7: First PCR Amplification (TruSeq RNA Access v2.0)

Master Step Name = First PCR Amplification (TruSeq RNA Access v2.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1

The version of First PCR Amplification 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 = Row

Record Details

Step Data (Master Step Fields)

Step 8: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1

Automations

Generate Bioanalyzer Input 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

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

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, Calculate nM and assign QC flags

Trigger Location = Not Used

Parse Bioanalyzer XML, Copy nM and Assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Targeted RNA Expression Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

Step Data
- Group of Defaults = TruSeq RNA Access Library Validation
- Master Step Fields

Step 9: First Hybridization (TruSeq RNA Access v2.0)

Master Step Name = Hybridize with Pooling v2.0
Step Type = Pooling
Aliquot Generation = Fixed, 1

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

Pooling

Label Uniqueness = On
Defaults
- Sample Grouping = Group by Containers

Placement

Defaults
- Well Sort Order = Row
- Placement Pattern = Column

Record Details

Step Data (Master Step Fields)

Step 10: First Capture (TruSeq RNA Access v2.0)

Master Step Name = Capture Hybridized Probes v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1

Automations

Calculate Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

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

Record Details

Step Data (Master Step Fields)

Step 11: Second Hybridization (TruSeq RNA Access v2.0)

Master Step Name = Perform Second Hybridization v2.0
Step Type = No Outputs
Reagent Kits

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

Record Details

Step Data (Master Step Fields)

Step 12: Second Capture (TruSeq RNA Access v2.0)

Master Step Name = Perform Second Capture v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1

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

Record Details

Step Data (Master Step Fields)

Step 13: Capture Sample Clean Up (TruSeq RNA Access v2.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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

Record Details

Step Data (Master Step Fields)

Step 14: Second PCR Amplification (TruSeq RNA Access v2.0)

Master Step Name = Second PCR Amplification v1.0
Step Type = No Outputs
Reagent Kits

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

Record Details

Step Data (Master Step Fields)

Step 15: Second PCR Clean Up (TruSeq RNA Access v2.0)

Master Step Name = Clean Up v2.0
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Manual button

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Step 16: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1

Automations

Generate Bioanalyzer Input file

Trigger Location = Record Details
Trigger Style = Automatic upon entry

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Record Details
Trigger Style = Manual button

Parse Bioanalyzer XML, Calculate 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, Copy nM and Assign QC flags

Trigger Location = Not Used

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSeq Targeted RNA Expression Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp

Step Data
- Group of Defaults = TruSeq RNA Access Library Validation
- Master Step Fields

Step 17: Normalize Libraries (TruSeq RNA Access v2.0)

Master Step Name = Normalize Libraries 1 v2.0.10
Step Type = Standard
Derived Sample Generation = Fixed, 1

The version of Normalized Libraries 1 master step name may be different depending on the version of IPP installed.

Automations

Normalization Calculations - Option 1

Trigger Location = Record Details
Trigger Style = Manual button

Set Next Step - Remove

Trigger Location = Record Details
Trigger Style = Automatic upon exit

Routing script - Normalize Libraries

Trigger Location = Step
Trigger Style = Automatic upon exit

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row

Record Details

Step Data (Master Step Fields)

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Category

Reagent Kits

TruSeq RNA Access - 12 Index Set A or B, Box 2
- Supplier = Illumina
- Catalog Number = Set A Part # 15052311; Set B Part # 15052312
- Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Placement Pattern = Row

Destination Containers

96 well plate

Default = Elution 2 - Frag - Prime

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

TruSeq RNA Access - cDNA Synthesis-PCR, Box 1

Supplier = Illumina
Catalog Number = 15052309
Website = https://support.illumina.com/

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Presets
- Synthesize 1st Strand
- 1stSS

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {SubmittedSampleName}

Reagent Kits

TruSeq RNA Access - cDNA Synthesis-PCR, Box 1
- Supplier = Illumina
- Catalog Number = 15052309
- Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Column
Table Columns - Global Fields

TruSeq RNA Access - 12 Index Set A or B, Box 2

Supplier = Illumina
Catalog Number = Set A Part # 15052311; Set B Part # 15052312
Website = https://support.illumina.com/

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Column
Table Columns - Global Fields

Naming Convention = {SubmittedSampleName}

Reagent Kits

TruSeq RNA Access - 12 Index Set A or B, Box 2
- Supplier = Illumina
- Catalog Number = Set A Part # 15052311; Set B Part # 15052312
- Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {SubmittedSampleName}

Reagent Kits

TruSeq RNA Access - cDNA Synthesis-PCR, Box 1
- Supplier = Illumina
- Catalog Number = 15052309
- Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Thermal Cycler Program

Text

Default = PCR

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {InputItemName} Bioanalyzer

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

Placement Pattern = Column

Destination Containers

BioAnalyzer DNA High Sensitivity Chip

BioAnalyzer DNA 1000 Chip

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,500.00

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 400.00

Criteria 1 - Threshold Value = 250.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,000.00

Criteria 1 - Threshold Value = 350.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,000.00

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 400.00

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

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 300.00

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 500.00

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 320.00

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 320.00

Criteria 1 - Threshold Value = 100.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 200.00

Criteria 1 - Threshold Value = 250.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 275.00

Criteria 1 - Threshold Value = 250.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 275.00

Criteria 1 - Threshold Value = 100.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 300.00

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Size - bp

Criteria 2 - Threshold Value = 400.00

Criteria 1 - Threshold Value = 160.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Size - bp

Criteria 2 - Threshold Value = 700.00

Criteria 1 - Threshold Value = 300.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Size - bp

Criteria 2 - Threshold Value = 400.00

Additional Options and Dropdown Items

Criteria 1 - Operator

Text Dropdown

Custom Entries

Presets

Criteria 1 - Source Data Field

Text Dropdown

Presets

Concentration
Conc. Units
Number of Peaks found

Criteria 1 - Threshold Value

Numeric

Decimal Places Displayed = 2

Criteria 2 - Operator

Text Dropdown

Custom Entries

Presets

Criteria 2 - Source Data Field

Text Dropdown

Presets

Concentration
Conc. Units
Number of Peaks found

Criteria 2 - Threshold Value

Numeric

Decimal Places Displayed = 2

Use strict matching for Bioanalyzer results

Toggle Switch

Default = None Set

Step File Placeholders

Bioanalyzer Input File - Automatically attached
Bioanalyzer Input 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 = Column
File Column Options
- File Column Display = Hide
- File Attachment Method = Auto
Table Columns - Global Fields

Naming Convention = {PoolName}

Reagent Kits

TruSeq RNA Access - Coding Transcriptome, Box 4
- Supplier = Illumina
- Catalog Number = 15052314
- Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Well Sort Order = Row

Destination Containers

Presets

RNA HYB
NRC HYB

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {InputItemName}

Reagent Kits

TruSeq RNA Access - Coding Capture Reagents, Box 3
- Supplier = Illumina
- Catalog Number = 15052313
- Website =
TruSeq RNA Access - Coding Transcriptome, Box 4
- Supplier = Illumina
- Catalog Number = 15052314

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Decimal Places Displayed = 2

2N NaOH (ul)

Numeric

Decimal Places Displayed = 2

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

TruSeq RNA Access - 12 Index Set A or B, Box 2

Supplier = Illumina
Catalog Number = Set A Part # 15052311; Set B Part # 15052312
Website = https://support.illumina.com/

TruSeq RNA Access - Coding Transcriptome, Box 4

Supplier = Illumina
Catalog Number = 15052314
Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {InputItemName}

Reagent Kits

TruSeq RNA Access - Coding Capture Reagents, Box 3
- Supplier = Illumina
- Catalog Number = 15052313
- Website =
TruSeq RNA Access - Coding Transcriptome, Box 4
- Supplier = Illumina
- Catalog Number = 15052314

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Reagent Kits

AMPure XP Beads
- Supplier = Beckman Coulter Genomics
- Catalog Number = A63881
- Website =
TruSeq RNA Access - 12 Index Set A or B, Box 2
- Supplier = Illumina
- Catalog Number = Set A Part # 15052311; Set B Part # 15052312

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

TruSeq RNA Access - cDNA Synthesis-PCR, Box 1

Supplier = Illumina
Catalog Number = 15052309
Website = https://support.illumina.com/

TruSeq RNA Access - Coding Transcriptome, Box 4

Supplier = Illumina
Catalog Number = 15052314
Website =

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Reagent Kits

AMPure XP Beads
- Supplier = Beckman Coulter Genomics
- Catalog Number = A63881
- Website =
TruSeq RNA Access - 12 Index Set A or B, Box 2
- Supplier = Illumina
- Catalog Number = Set A Part # 15052311; Set B Part # 15052312

Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields

Step File Placeholders

Log File - Automatically attached

Sample Table

Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields

Naming Convention = {InputItemName} Bioanalyzer

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

Placement Pattern = Column

Destination Containers

BioAnalyzer DNA High Sensitivity Chip

BioAnalyzer DNA 1000 Chip

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,500.00

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 400.00

Criteria 1 - Threshold Value = 250.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,000.00

Criteria 1 - Threshold Value = 350.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 1,000.00

Criteria 1 - Threshold Value = 150.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Region 1 Average Size - bp

Criteria 2 - Threshold Value = 400.00

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

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 300.00

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

Criteria 2 - Source Data Field = Peak 2 Size - bp

Criteria 2 - Threshold Value = 500.00

Criteria 1 - Threshold Value = 200.00

Criteria 2 - Operator = <=

TruSeq RNA Access v2.0

hashtagOverview

hashtagProtocol 1: TruSeq RNA Access v2.0

hashtagStep 1: Sort Samples (TruSeq RNA Access v2.0)

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 2: Fragment RNA (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement

hashtagRecord Details

hashtagStep 3: First Strand cDNA Synthesis (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 4: Second Strand cDNA Synthesis (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 5: Adenylate 3' Ends (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 6: Ligate Adapters (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagAdd Labels

hashtagRecord Details

hashtagStep 7: First PCR Amplification (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 8: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagRecord Details

hashtagStep 9: First Hybridization (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPooling

hashtagPlacement

hashtagRecord Details

hashtagStep 10: First Capture (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 11: Second Hybridization (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 12: Second Capture (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 13: Capture Sample Clean Up (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 14: Second PCR Amplification (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 15: Second PCR Clean Up (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

hashtagStep 16: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagPlacement = Enabled

hashtagRecord Details

hashtagStep 17: Normalize Libraries (TruSeq RNA Access v2.0)

hashtagAutomations

hashtagQueue/Ice Bucket

hashtagRecord Details

Overview

Protocol 1: TruSeq RNA Access v2.0

Step 1: Sort Samples (TruSeq RNA Access v2.0)

Queue/Ice Bucket

Record Details

Step 2: Fragment RNA (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Placement

Record Details

Step 3: First Strand cDNA Synthesis (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 4: Second Strand cDNA Synthesis (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 5: Adenylate 3' Ends (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 6: Ligate Adapters (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Add Labels

Record Details

Step 7: First PCR Amplification (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 8: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 9: First Hybridization (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Pooling

Placement

Record Details

Step 10: First Capture (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 11: Second Hybridization (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 12: Second Capture (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 13: Capture Sample Clean Up (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 14: Second PCR Amplification (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 15: Second PCR Clean Up (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details

Step 16: Bioanalyzer QC (Library Validation) (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Placement = Enabled

Record Details

Step 17: Normalize Libraries (TruSeq RNA Access v2.0)

Automations

Queue/Ice Bucket

Record Details