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
