The Respiratory Virus Panel workflow includes the following functionality:
Preconfigured protocols that support the preparation of upper and lower respiratory specimens for real-time RT-PCR qualitative detection of nucleic acid from the 2019-nCoV.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
Routing to iSeq, MiniSeq, MiSeq, NextSeq 550, NextSeq 2000.
Protocol 1: Sort Sample Type (Respiratory Virus Panel v1.0)
Protocol Type = Other
Next Steps Configuration
Step 1: Sort Sample Type (Respiratory Virus Panel v1.0)
Master Step Name = Sort Sample Type (Respiratory Virus Panel v1.0)
Master Step Name = Second-Strand Synthesis (Respiratory Virus Panel v1.0)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Sample Type - ds cDNA output
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Remove
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing Script - Nextera Flex for Enrichment OUTPUTS
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step File Placeholders
Log File - Automatically attached
Sample Table
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Naming Convention = {InputItemName}
ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
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
Default =
Add up to 3.5 ml of sample to the microconcentrator
Centrifuge to a final volume of 140 μl.
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
Buffer AW1
Catalog Number = 61904
Buffer AW2
Catalog Number = 61904
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
Decimal Places Displayed = 2
Carrier RNA AVE Volume (uL)
Numeric
Decimal Places Displayed = 2
Incubation End Time:
Text
Incubation Start Time:
Text
Total Samples
Numeric
Default = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Column
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Buffer AW1
Catalog Number = 61904
Buffer AW2
Catalog Number = 61904
QIAvac 24 Plus vacuum manifold
Catalog Number = 19413
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
Decimal Places Displayed = 2
Carrier RNA AVE Volume (uL)
Numeric
Decimal Places Displayed = 2
Incubation End Time:
Text
Incubation Start Time:
Text
Total Samples
Numeric
Default = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
ℹ The actual version of the Prep Samples - Bead Beating and Prep Samples steps may be different depending on the version of IPP installed.
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
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
Naming Convention = {InputItemName}
Reagent Kits
AllPrep PowerViral DNA/RNA Kit
β-mercaptoethanol
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
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
AllPrep PowerViral DNA/RNA Kit
Phenol:chloroform:isoamyl alcohol
Supplier = supplied by user
β-mercaptoethanol
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
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
Maxima H Minus Double-Stranded cDNA Synthesis Kit
Supplier = K2561
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
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Maxima H Minus Double-Stranded cDNA Synthesis Kit
Supplier = K2561
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
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Decimal Places Displayed = 2
Second Strand Enzyme Mix (uL)
Numeric
Decimal Places Displayed = 2
Total Volume (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
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
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
GeneJET PCR Purification Kit
Catalog Number = K0701, K0702
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
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
Naming Convention = {InputItemName}
Reagent Kits
NEBNext First Strand Synthesis Reaction Buffer
Supplier = NEB
Catalog Number = E7525S, E7525L
NEBNext Poly(A) mRNA Magnetic Isolation Module
Supplier = NEB
Catalog Number = E7490S, E7490L
NEBNext Random Primers
Supplier = NEB
Catalog Number = S1330S
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
Decimal Places Displayed = 2
MM1: NEBNext First Strand Synthesis Reaction Buff (uL)
Numeric
Decimal Places Displayed = 2
MM1: NEBNext Random Primers (uL)
Numeric
Decimal Places Displayed = 2
MM1: Nuclease-free Water (uL)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Naming Convention = {InputItemName}
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
Decimal Places Displayed = 2
ProtoScript II Reverse Transcriptase (uL)
Numeric
Decimal Places Displayed = 2
Thermal Cycler Program
Multiline Text
Default =
10 minutes at 25°C
50 minutes at 42°C
15 minutes at 70°C
Hold at 4°C
Total Samples
Numeric
Default = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
Supplier = NEB
Catalog Number = E6111S, E6111L
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
Decimal Places Displayed = 2
NEBNext Second Strand Synthesis Enzyme Mix (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Step File Placeholders
Log File - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module
Supplier = NEB
Catalog Number = E6111S, E6111L
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
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
Naming Convention = {InputItemName}
Reagent Kits
SuperScript Double-Stranded cDNA Synthesis Kit
Catalog Number = 11917-010, 11917-020
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
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
SuperScript Double-Stranded cDNA Synthesis Kit
Catalog Number = 11917-010, 11917-020
ℹ The actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
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
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
Field Name
Field Type
Options
Additional Options and Dropdown Items
Instruction
Multiline Text
Read Only
Default = Please select the Respiratory Virus Extraction Protocol for each sample.
Field Name
Field Type
Options
Additional Options and Dropdown Items
Sample Volume (mL)
Numeric
Default = 3.5
Directions
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
96-100% EtOH Prep Date
Date
Buffer AVL Volume (ml)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
96-100% EtOH Prep Date
Date
Buffer AVL Volume (ml)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
100% EtOH Open Date
Date
Field Name
Field Type
Options
Additional Options and Dropdown Items
100% EtOH Open Date
Date
Field Name
Field Type
Options
Additional Options and Dropdown Items
Directions
Multiline Text
Default = Please record the volumes for the following fields: Volume of Oligo(dT)18 Used (uL), Volume of Template RNA Used (uL), Nuclease-free Water Used (uL).
Field Name
Field Type
Options
Additional Options and Dropdown Items
5x Second Strand Reaction Mix (uL)
Numeric
Decimal Places Displayed = 2
First Strand cDNA Synthesis (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
RNase I (uL) to add to each tube
Numeric
Default = 10
Field Name
Field Type
Options
Additional Options and Dropdown Items
Beads MM: Oligo dT Beads d(T)25 (uL)
Numeric
Decimal Places Displayed = 2
Beads MM: RNA Binding Buffer (2X) (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Murine RNase Inhibitor (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
First-Strand Synthesis Product Volume per Well (uL)
Numeric
Default = 20
NEBNext Second Strand Reaction Buffer (uL)
Numeric
Field Name
Field Type
Options
Additional Options and Dropdown Items
Directions
Multiline Text
Default = Please enter ug of starting mRNA or Total RNA and Prep Sample Type in field below.
