The DNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel is part of the AmpliSeq for Illumina Childhood Cancer Panel protocols that include the following functionality:
Preconfigured AmpliSeq for Illumina Childhood Cancer Panel protocol that supports the preparation of up to 384 uniquely indexed libraries of genomic DNA or total RNA using the AmpliSeq for Illumina workflow.
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.
There is no extraction protocol in this workflow because the samples are already extracted.
Protocol 1: DNA Library Prep (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute DNA (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 2: Qubit (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Step Type = Standard QC
Measurement Generation = Fixed, 1
Automations
Assign QC flags (Qubit QC)
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step and Copy Concentration
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration and Set Sample Volume
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 4: Amplify DNA Targets (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Amplify Targets Duplicates (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 2
Automations
Copy Concentration, Total Volume and Input Amount
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Prep Input - CCP
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Calculate Prep Input - Myeloid Panel
Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Group of Defaults
Childhood Cancer Panel
Recommended Prep Input (ng) = This protocol supports 1-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Thermal Cycler Program = AMP
Myeloid Panel
Recommended Prep Input (ng) = This protocol supports 10-100 ng per pool. The recommended input is 10 ng high-quality DNA per pool.
Thermal Cycler Program = AMP
Step Data
Group of Defaults = Childhood Cancer Panel
Master Step Fields
Step 5: Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Transfer RNA and DNA Amplicons (AmpliSeq for Illumina v1.1)
Step Type = Pooling
Aliquot Generation = Fixed, 1
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Pooling
Label Uniqueness = Off
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Well Sort Order = Row
Placement Pattern = Column
Record Details
Step File Placeholders
Log - Automatically attached
Sample Table
Step 6: Partially Digested Amplicons (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Step 7: Ligate Indexes (AmpliSeq for Illumina Childhood Cancer Panel v1.1)
Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Route AmpliSeq Samples - Childhood Cancer Panel
Trigger Location = Step
Trigger Style = Automatic upon exit
Route AmpliSeq Samples - Immune Repertoire Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - BRCA
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CHP v2
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - CP
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Custom DNA Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Focus Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Immune Response Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples - Myeloid Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Route AmpliSeq Samples -Transcriptome Human GEx Panel
Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
