Roche MagNA Pure 96 v1.1

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Last updated 1 month ago

Overview

The Roche MagNA Pure 96 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: Roche MagNa Pure 96 (CDC COVID-19 RT-PCR v1.1)

Protocol Type = Sample Prep

Next Steps Configuration

Step 1: Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Sort Roche MagNA Pure 96 (CDC COVID-19 RT-PCR v1.1)
Step Type = No Outputs

Automations

Set Next Step - Roche MagNA Pure 96

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.::MagNA Pure 96 Sample Type:: == ::Whole blood::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Plasma::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Serum::) {nextStep = ::Lysates (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Bacteria::) {nextStep = ::Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Stool::) {nextStep = ::Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Swabs::) {nextStep = ::Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Cultured Cells::) {nextStep = ::Cultured Cells (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::Fresh-frozen Tissue::) {nextStep = ::Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)::} ; \
if (input.::MagNA Pure 96 Sample Type:: == ::FFPE::) {nextStep = ::Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)::} ' \
-log {compoundinputFileLuid0}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 2: Lysates (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Lysates (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNA Pure 96 External Lysis Buffer
  - Catalog Number = 06374913001

Automations

Calculate Lysed Sample (uL)

Trigger Location = Record Details
Trigger Style = Manual button

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 'output.::Lysed Sample (uL):: = output.::Starting Sample Volume (uL):: + output.::External Lysis Buffer (uL)::' \
-log {compoundinputFileLuid0}"

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Placement = Enabled

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

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 3: Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Lysis Protocol using MagNA Pure 96 Bacterial Lysis Buffer (BLB) (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNA Pure 96 Bacterial Lysis Buffer
  - Catalog Number = 06374921001
- PBS
- Proteinase K
  - Catalog Number = 03 115 828 001

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Placement = Enabled

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

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Pretreatment of Stool Samples (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNA Pure 96 Bacterial Lysis Buffer
  - Catalog Number = 06374921001
- Proteinase K
  - Catalog Number = 03 115 828 001

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Record Details

Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 5: Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Pretreatment of Swabs (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNA Pure 96 Bacterial Lysis Buffer
  - Catalog Number = 06374921001
- PBS
- Proteinase K
  - Catalog Number = 03 115 828 001

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Placement = Enabled

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

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Cultured Cells (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Cultured Cells (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- PBS

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Placement = Enabled

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

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 7: Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Fresh-frozen Tissue Sorting (CDC COVID-19 RT-PCR v1.1)
Step Type = No Outputs

Automations

Set Next Step - Fresh-frozen Tissue

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.::Homogenization Protocol:: == ::Proteinase K Digestion::) {nextStep = ::Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)::} else {nextStep = ::Tissue Homogenization using MagNA Lyser Instrument (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)

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 8: Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Tissue Homogenization by Proteinase K Digestion (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNa Pure 96 DNA Tissue Lysis Buffer
  - Catalog Number = 06640702001
- Proteinase K
  - Catalog Number = 03 115 828 001

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 9: Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Tissue Homogenization using MagNA Lyser Instrument (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNA Lyser Green Beads
  - Catalog Number = 03358941001
- MagNa Pure 96 DNA Tissue Lysis Buffer
  - Catalog Number = 06640702001

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Record Details

Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 10: Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Deparaffinization of FFPE Tissue Sections (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
- MagNa Pure 96 DNA Tissue Lysis Buffer
  - Catalog Number = 06640702001
- Proteinase K
  - Catalog Number = 03 115 828 001
- Xylol

Automations

Set Next Step - Purification MagNa Pure 96

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 = ::Isolation Procedure (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)

Record Details

Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 11: Isolation Procedure (CDC COVID-19 RT-PCR v1.1)

Master Step Name = Isolation Procedure (CDC COVID-19 RT-PCR v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}

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)

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)
Step File Placeholders
- Log - Automatically attached
Sample Table
- Sample Display Default = Exp