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Roche MagNA Pure 96 v1.1

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Last updated 17 days 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}"

ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.

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 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
  MagNA Pure 96 Sample Type
  Text Dropdown
  Required Field
  Presets
  Whole blood
  Plasma
  Serum
  Bacteria
  Stool
  Swabs
  Cultured Cells
  Fresh-frozen Tissue
  FFPE
  Derived Sample
  Sample Name
  Built-in

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}"

ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.

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
- 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
  Category
  Field Name
  Field Type
  Options
  Additional Options and Dropdown Items
  Derived Sample
  External Lysis Buffer (uL)
  Numeric
  Default = 200
  Derived Sample
  Lysed Sample (uL)
  Numeric
  Derived Sample
  Sample Name
  Built-in
  Derived Sample
  Starting Sample Volume (uL)
  Numeric Dropdown
  Required Field
  Custom Entries
  Presets
  50
  100
  200

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}"

ℹ The version of the step name for nextStep may be different depending on the version of IPP installed.

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
- 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
  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 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