In Clarity LIMS, protocols for QC and Sample Preparation include modules to increase accuracy and facilitate management of the complex library prep components.
Each step includes a graphical interface to facilitate tube-to-plate and plate-to-plate transfers.
Each step tracks the user, time, and date of each task being completed in the lab.
Each step allows printing a sample or plate manifest to use as needed.
In Clarity LIMS, you can track lot numbers, kit numbers, and other conditions for each laboratory process.
RNA Initial QC 5.1.2
Overview
The initial RNA QC protocol contains steps to track quality control data from commonly used QC instruments. Through data integrations, QC data can be added to Clarity LIMS directly from the instrument outputs.
Highlights of this protocol include:
Data integrations for Bioanalyzer 2100, Nanodrop 8000, CaliperGX, and Tapestation 2200, including creation of the input file and parsing of data output.
Assignment of pass/fail QC based on chosen criteria.
Aggregation of data from multiple QC steps.
Protocol 1: RNA Initial QC 5.1.2
Protocol Type = QC
Capacity = 50
QC Filters
Step: Bioanalyzer QC (RNA) 5.1.2
Master Step Name = Bioanalyzer QC (RNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
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 Projects
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Step Data
Step Data Heading = Begin by uploading the required Bioanalyzer XML result file
Master Step Fields
Step: NanoDrop QC (RNA) 5.1.2
Master Step Name = NanoDrop QC (RNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Generate NanoDrop driver file
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse NanoDrop NDT and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Step Data
Step Data Heading = Begin by uploading the required NanoDrop NDT result file
Master Step Fields
Step: Qubit QC (RNA) 5.1.2
Master Step Name = Qubit QC (RNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Step Data
Step Data Heading = Begin by completing the Sample Details table
Master Step Fields
Step: PicoGreen QC (RNA) 5.1.2
Master Step Name = PicoGreen QC (RNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Step Data
Step Data Heading = Begin by completing the Sample Details table
Master Step Fields
Step: CaliperGX QC 5.1.2
Master Step Name = CaliperGX QC 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} CaliperGX
Automations
Generate Driver File
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse CaliperGX CSV
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
Caliper Defaults
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration
Step Data
Group of Defaults = Caliper Defaults
Master Step Fields
Step: Tapestation QC (RNA) 5.1.2
Master Step Name = Tapestation QC (RNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Generate Tapestation Input Sampletable CSV
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Tapestation XML and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step: Aggregate QC (RNA) 5.1.2
Master Step Name = Aggregate QC (RNA) 5.1.2
Step Type = No Outputs
Automations
Aggregate QC Flags and Copy Fields
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
CaliperGX Values
Bioanalzyer QC (RNA) 5.1.2 = Use if available (Priority 5)
CaliperGX QC 5.1.2 = Use if available (Priority 5)
Step Data
Step Data Heading = Begin by verifying copy tasks and aggregation priorities
Group of Defaults = CaliperGX Values
DNA Initial QC 5.1.2
Overview
The initial DNA QC protocol contains steps to track quality control data from commonly used QC instruments. Through data integrations, QC data can be added to Clarity LIMS directly from the instrument outputs.
Highlights of this protocol include:
Data integrations for Bioanalyzer 2100, Nanodrop 8000, CaliperGX, and Tapestation 2200, including creation of the input file and parsing of data output.
Assignment of pass/fail QC based on chosen criteria.
Aggregation of data from multiple QC steps.
Protocol 1: DNA Initial QC 5.1.2
Protocol Type = QC
Capacity = 100
QC Filters
Step: Bioanalyzer QC (DNA) 5.1.2
Master Step Name = Bioanalyzer QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
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
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Output PASS/FAIL
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step and Copy to Input
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
NRCC
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Peak 2 Size Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq ChIP-Seq
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Molarity
TruSeq Methyl Capture EPIC
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Rapid Exome
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Step Data
Step Data Heading = Begin by uploading the required Bioanalyzer XML result file
Group of Defaults = Peak 2 Size Thresholds
Step: NanoDrop QC (DNA) 5.1.2
Master Step Name = NanoDrop QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Generate NanoDrop driver file
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse NanoDrop NDT and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
A260/A280 Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = A260/280 ratio
Step Data
Step Data Heading = Begin by uploading the required NanoDrop NDT result file
Group of Defaults = A260/A280 Thresholds
Step: Qubit QC (DNA) 5.1.2
Master Step Name = Qubit QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
Concentration Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration
Step Data
Step Data Heading = Begin by completing the Sample Details table
Group of Defaults = Concentration Thresholds
Step: PicoGreen QC (DNA) 5.1.2
Master Step Name = PicoGreen QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
Concentration Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration
Step Data
Step Data Heading = Begin by completing the Sample Details table
Group of Defaults = Concentration Thresholds
Step: CaliperGX QC 5.1.2
Master Step Name = CaliperGX QC 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} CaliperGX
Automations
Generate Driver File
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse CaliperGX CSV
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
Caliper Defaults
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration
Step Data
Group of Defaults = Caliper Defaults
Master Step Fields
Step: Tapestation QC (DNA) 5.1.2
Master Step Name = Tapestation QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Generate Tapestation Input Sampletable CSV
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Tapestation XML and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
Peak 2 Size Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 MW
Step Data
Group of Defaults = Peak 2 Size Thresholds
Master Step Fields
Step: Aggregate QC (DNA) 5.1.2
Master Step Name = Aggregate QC (DNA) 5.1.2
Step Type = No Outputs
Automations
Aggregate QC Flags and Copy Fields
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Projects
Well Sort Order = Row
Record Details
Group of Defaults
NanoDrop Values
Bioanalzyer QC (DNA) 5.1.2 = Use if available (Priority 5)
CaliperGX QC 5.1.2 = Use if available (Priority 5)
Step Data
Step Data Heading = Begin by verifying copy tasks and aggregation priorities
The Library Validation QC protocol contains steps to track quality control data from commonly used QC instruments. Through data integrations, QC data can be added to Clarity LIMS directly from the instrument outputs.
Highlights of this protocol include:
Data integrations for Bioanalyzer 2100 and Tapestation 2200, including creation of the input file and parsing of data output.
Possible integrations with qPCR instruments: TaqMan 7900 or ViiA7.
Assignment of pass/fail QC based on chosen criteria.
Aggregation of data from multiple QC steps.
Protocol 1: Library Validation QC 5.1.2
Protocol Type = QC
Capacity = 50
QC Filters
Step: Bioanalyzer QC (DNA) 5.1.2
Master Step Name = Bioanalyzer QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
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
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Output PASS/FAIL
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step and Copy to Input
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Previous Steps
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
NRCC
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Peak 2 Size Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq ChIP-Seq
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Molarity
TruSeq Methyl Capture EPIC
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
TruSeq Rapid Exome
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Step Data
Step Data Heading = Begin by uploading the required Bioanalyzer XML result file
Group of Defaults = Peak 2 Size Thresholds
Step: qPCR QC 5.1.2
Master Step Name = qPCR QC 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} qPCR
Automations
Assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Previous Steps
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
Concentration Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Concentration
Step Data
Step Data Heading = Begin by completing the Sample Details table
Group of Defaults = Concentration Thresholds
Step: Tapestation QC (DNA) 5.1.2
Master Step Name = Tapestation QC (DNA) 5.1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Generate Tapestation Input Sampletable CSV
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Parse Tapestation XML and assign QC flags
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Previous Steps
Well Sort Order = Row
Record Details
Group of Defaults
Peak 2 Size Thresholds
Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 MW
Step Data
Group of Defaults = Peak 2 Size Thresholds
Master Step Fields
Step: Aggregate QC (Library Validation) 5.1.2
Master Step Name = Aggregate QC (Library Validation) 5.1.2
Step Type = No Outputs
Automations
Aggregate QC Flags and Copy Fields
Trigger Location = Record Details
Trigger Style = Manual button
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Previous Steps
Well Sort Order = Row
Record Details
Group of Defaults
Tapestation Values
Bioanalzyer QC (DNA) 5.1.2 = Use if available (Priority 5)
Copy task 1 - Source Field = Concentration
Step Data
Step Data Heading = Begin by verifying copy tasks and aggregation priorities
Group of Defaults = Tapestation Values
Bioanalyzer QC (DNA) 5.1.2
Did not pass - Bioanalyzer QC (DNA) 5.1.2
qPCR QC 5.1.2
Did not pass - qPCR QC 5.1.2
Tapestation QC (DNA) 5.1.2
Did not pass - Tapestation QC (DNA) 5.1.2
Aggregate QC (Library Validation) 5.1.2
Passed - Bioanalyzer QC (DNA) 5.1.2 OR
Passed - qPCR QC 5.1.2 OR
Passed - Tapestation QC (DNA) 5.1.2
Naming Convention = {InputItemName} Bioanalyzer
Sample Table
Column Headers
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Expanded View Fields
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 = 1,000.00
Use strict matching for Bioanalyzer results = No
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
Criteria 1 - Threshold Value = 5.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Molarity
