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bioMerieux NucliSENS easyMAG Instrument v1.1

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Last updated 17 days ago

Overview

The bioMerieux NucliSENS easyMAG Instrument CDC COVID-19 RT-PCR is part of the CDC COVID-19 RT-PCR protocols that include the following functionality.

Preconfigured CDC COVID-19 RT-PCR 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.

Protocol 1: bioMérieux NucliSENS easyMAG Instrument (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Nucleic Acid Extraction (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Nucleic Acid Extraction (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- easyMAG Lysis Buffer
  - Catalog Number = 200292
- easyMAG Wash Buffers 1, 2 and 3

Automations

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
      script:evaluateDynamicExpression \
      -t false \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Directions
Multiline Text
Default = Add 100 uL of sample to 1000 uL of pre-aliquoted easyMAG lysis buffer (total input sample volume is 1100 uL)
Incubation Finish Time
Text
Incubation Start Time
Text
Step File Placeholders
- Log - Automatically attached
Sample Table
- 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
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Protocol 2: Real-Time RT-PCR Prep (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Assay Set Up Sorting (CDC COVID-19 RT-PCR v1.1)
Step Type = No Outputs

Automations

Set Next Step - RT-qPCR

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'if (input.::RT-qPCR Assay:: == ::Thermofisher TaqPath 1-Step RT-qPCR::) {nextStep = ::Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)::}  ; if (input.::RT-qPCR Assay:: == ::Promega GoTaq Probe 1-Step RT qPCR::) {nextStep = ::Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix::) {nextStep = ::Quantabio qScript XLT One-Step RT-qPCR Tough Mix (CDC COVID-19 RT-PCR v1.1)::} ; if (input.::RT-qPCR Assay:: == ::Quantabio UltraPlex 1-Step ToughMix (4X)::) {nextStep = ::Quantabio UltraPlex 1-Step ToughMix (4X) (CDC COVID-19 RT-PCR v1.1)::}' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Derived Sample
  RT-qPCR Assay
  Text Dropdown
  Required Field
  Presets
  Thermofisher TaqPath 1-Step RT-qPCR
  Promega GoTaq Probe 1-Step RT qPCR
  Quantabio qScript XLT One-Step RT-qPCR Tough Mix
  Quantabio UltraPlex 1-Step ToughMix (4X)
  Derived Sample
  Sample Name
  Built-in

Step 2: Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Thermofisher TaqPath 1-Step RT-qPCR (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
- Thermofisher TaqPath 1-Step RT-qPCR Master Mix, CG
  - Supplier = Thermofisher
  - Catalog Number = A15299; A15300
Control Types
- HSC
- nCoVPC
- NTC

Automations

auto placement for 7500 Covid-19 assay

Trigger Location = Placement
Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 8.5 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::TaqPath 1-Step RT-qPCR Master Mix (4x) (uL):: = step.::Total Samples:: * 5 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Decimal Places Displayed = 2
TaqPath 1-Step RT-qPCR Master Mix (4x) (uL)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Total Volume (uL)
Numeric
Decimal Places Displayed = 2
Step File Placeholders
- Log - Automatically attached
Sample Table
- 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
  LIMS ID (Container)
  Built-in
  Container
  Well
  Built-in
  Derived Sample
  Sample Name
  Built-in
  Project
  Project Name
  Built-in

Step 3: Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Promega GoTaq Probe 1-Step RT qPCR (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 3
Naming Convention = {InputItemName}-{LIST:N1,N2,P}
Reagent Kits
- Promega GoTaq Probe 1- Step RT-qPCR System
  - Catalog Number = A6120; A6121
Control Types
- HSC
- nCoVPC
- NTC

Automations

auto placement for 7500 Covid-19 assay

Trigger Location = Placement
Trigger Style = Automatic upon entry

/usr/bin/python3 /opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}

Calculate Total Samples and Master Mix

Trigger Location = Record Details
Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Nuclease-free Water (uL):: = step.::Total Samples:: * 3.1 ; \
step.::Combined Primer/Probe Mix (uL):: = step.::Total Samples:: * 1.5 ; \
step.::GoTaq Probe qPCR Master Mix with dUTP (uL):: = step.::Total Samples:: * 10 ; \
step.::Go Script RT Mix for 1-Step RT-qPCR (uL):: = step.::Total Samples:: * 0.4 ; \
step.::Total Volume (uL):: = step.::Total Samples:: * 15' \
-log {compoundOutputFileLuid0}"

Set Next Step - RT-qPCR Assay

Trigger Location = Record Details
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'nextStep = ::ABI 7500 Fast DX (CDC COVID-19 RT-PCR v1.1)::' \
-log {compoundOutputFileLuid0}"

ℹ The version of ABI 7500 Fast DX step name may be different depending on the version of IPP installed.

copy PCR Product LIMSID to Sample

Trigger Location = Step
Trigger Style = Automatic upon exit

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'submittedSample.::PCR Product LIMSID:: = input.node.@limsid' \
-log {compoundOutputFileLuid0}"

Queue/Ice Bucket

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

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
- Placement Pattern = Row
Destination Containers
- 96 well plate

Record Details

Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Combined Primer/Probe Mix (uL)
Numeric
Decimal Places Displayed = 2
Go Script RT Mix for 1-Step RT-qPCR (uL)
Numeric
Decimal Places Displayed = 2
GoTaq Probe qPCR Master Mix with dUTP (uL)
Numeric
Decimal Places Displayed = 2
Nuclease-free Water (uL)
Numeric
Decimal Places Displayed = 2
Total Samples
Numeric
Default = 0
Total Volume (uL)
Numeric