Illumina COVIDSeq v1.6
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The Illumina COVIDSeq Workflow workflow includes the following functionality:
Preset Illumina COVIDSeq Workflow protocols that track samples through the quantitative detection of SARS-CoV-2 RNA from nasopharyngeal (NP), oropharyngeal (OP), and nasal swab as well as mid-turbinate specimens collected from individuals who meet COVID-19 clinical or epidemiological criteria.
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.
Sample preparation for use on the NovaSeq 6000 Sequencing System.
Parsing of analysis results into Clarity LIMS.
Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Prep Sample (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Positive Control HT
Supplier = Illumina
Website = www.illumina.com
Illumina COVIDSeqTest Box 4
Supplier = Illumina
Catalog Number = 20043436
Website = www.illumina.com
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
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Instruction Notes
Multiline Text
Read Only
Default = For each sample, add 140 µl patient sample, dilution 3 CPC HT, or ELB HT (no template control) to a new 1.7 ml microcentrifuge tube.
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
Master Step Name = Spin Purification of RNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
QIAmp Viral RNA Mini kit
Supplier = Qiagen
Catalog Number = (50) - 52904; (250) - 52906
Website = https://www.qiagen.com
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
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
% EtOH
Numeric
Default = 96
Range = 96 To 100
% EtOH Prep Date
Date
AW1 Concentrate (mL)
Numeric
AW2 Concentrate (mL)
Numeric
Buffer AVL (mL)
Numeric
Decimal Places Displayed = 0
Carrier RNA-Buffer AVE (uL)
Numeric
Decimal Places Displayed = 0
Elution Incubation End Time
Numeric
Elution Incubation Start Time
Numeric
EtOH for AW1 (mL)
Numeric
EtOH for AW2 (mL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Enter in No. of Preps before clicking on "Calculate AW1, AW2, AVL Reagent Volumes". Elute in 30 µl Buffer AVE instead of 60 µl. Incubate elution for at least 1 minute.
No. of Preps
Numeric Dropdown
Required Field
Custom Entries
Presets
250
50
Default = 250
Total Samples
Numeric
Default = 0
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
Master Step Name = Anneal Sample (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 5 – 3072 Samples
Supplier = Illumina
Catalog Number = 20043648
Website = www.illumina.com
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
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq Anneal Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 17 µl 65°C for 3 minutes Hold at 4°C
Instruction Notes
Multiline Text
Read Only
Default = Add 8.5 µl EPH3 HT to each well. Add 8.5 µl eluted sample to each well. Seal and shake at 1600 rpm for 1 minute. Centrifuge at 1000 × g for 1 minute.
Thermal Cycler Program Notes
Text
Default = COVIDSeq Anneal
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
Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Synthesize First Strand cDNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 6 – 3072 Samples
Supplier = Illumina
Catalog Number = 20043647
Website = www.illumina.com
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
LIMS ID (Container)
Built-in
Container
Well
Built-in
Derived Sample
Sample Name
Built-in
Derived Sample
Waiting
Built-in
Project
Project Name
Built-in
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
COVIDSeq FSS Program Notes
Multiline Text
Read Only
Default = Choose the preheat lid option Set the reaction volume to 25 µl 25°C for 5 minutes 50°C for 10 minutes 80°C for 5 minutes Hold at 4°C
FSA (uL)
Numeric
Instruction Notes
Multiline Text
Read Only
Default = Add 8 µl First Strand cDNA Master Mix to each well of the CDNA1 plate.
RVT (uL)
Numeric
Total Samples
Numeric
Required Field
Default = 0
Thermal Cycler Program
Text
Default = COVIDSeq FSS
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
Protocol Type = Sample Prep
Next Steps Configuration
Master Step Name = Amplify cDNA (Illumina COVIDSeq Workflow v1.6)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
Illumina COVIDSeq Test Box 5 – 3072 Samples
Supplier = Illumina
Catalog Number = 20043648
Website = www.illumina.com
Illumina COVIDSEQ Test Box 7 – 3072 Samples
Supplier = Illumina
Catalog Number = 20043439
Website = www.illumina.com