The Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel is part of the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocols which include the following functionality:
Preconfigured AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of 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: Standard Workflow (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Clean Up Library (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 2: Amplify Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
Step Type = No Outputs
Reagent Kits
Automations
Count Samples and Calculate Master Mix
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Calculate Total Samples and Calculate Master Mix
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 3: Perform Second Clean Up (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)
The Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel is part of the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocols which include the following functionality:
Preconfigured AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of total RNA using the AmpliSeq for Illumina workflow.
The RNA Library Prep AmpliSeq for Illumina Transcriptome Human Gene Expression Panel is part of the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocols which include the following functionality:
Preconfigured AmpliSeq for Illumina Transcriptome Human Gene Expression Panel protocol that supports the preparation of up to 96 uniquely indexed libraries of 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: RNA Library Prep (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute RNA (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Dilute RNA (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 - RNA
Trigger Location = Record Details
Trigger Style = Manual button
Copy Desired Concentration
Trigger Location = Step
Trigger Style = Automatic upon exit
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 Transcriptome Human Gene Expression 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 RNA to Final Concentration (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Dilute RNA (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 - RNA
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Copy Desired Concentration
Trigger Location = Step
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: Reverse Transcribe (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Reverse Transcribe RNA (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Copy Concentration, Total Volume and Input Amount
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Calculate Input Amount - Transcriptome Human Genome Expression Panel
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Calculate Input Amount
Trigger Location = Not Used
Calculate Input Amount - Focus Panel
Trigger Location = Not Used
Calculate Input Amount - Immune Repertoire Panel
Trigger Location = Not Used
Calculate Input Amount - Immune Response Panel
Trigger Location = Not Used
Calculate Input Amount - Myeloid Panel
Trigger Location = Not Used
Calculate Input Amount - TCRbeta-SR
Trigger Location = Not Used
Calculate Input Amount- Custom RNA Panel
Trigger Location = Not Used
Copy Concentration, Total Volume and Input Amount - Myeloid
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
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Comprehensive Panel v3
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Focus Panel
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Immune Repertoire Panel
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Immune Response Panel
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Myeloid Panel
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
TCR beta-SR panel
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Transcriptome HGx
AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Step Data
Group of Defaults = Transcriptome HGx
Master Step Fields
Step 5: Amplify cDNA Targets (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)
Master Step Name = Amplify cDNA Targets Standard (AmpliSeq for Illumina v1.1)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Automations
Set Sample Type and Calculate Master Mix - TGx Panel
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Routing 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.
Routing Samples - TCRbeta SR 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.
Set Sample Type and Calculate Master Mix - Custom RNA
Trigger Location = Not Used
Set Sample Type and Calculate Master Mix - Immune Repertoire Panel
Trigger Location = Not Used
Set Sample Type and Calculate Master Mix - Immune Response Panel
Trigger Location = Not Used
Set Sample Type and Calculate Master Mix - Myeloid Panel
Trigger Location = Not Used
Set Sample Type and Calculate Master Mix - TCR beta-SR Panel
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 6: Partially Digested Amplicons (AmpliSeq for Illumina Transcriptome Human Gene Expression 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 Transcriptome Human Gene Expression 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 -Transcriptome Human GEx 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 - Childhood Cancer 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 - 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.
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
Add Labels
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
Record Details
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
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
Default = If enough RNA is available, dilute to intermediate concentration ~20-50 ng/uL.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Naming Convention = {InputItemName}
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
Default = Concentration
Criteria 1 - Threshold Value
Numeric
Criteria 2 - Operator
Text
Default = <=
Criteria 2 - Source Data Field
Text
Default = Concentration
Criteria 2 - Threshold Value
Numeric
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Automatically attached
Upload File - Manually uploaded
Sample Table
Enable QC Flags = Yes
Sample Display Default = Expand
Well Sort Order = Row
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName}
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
Default = If enough RNA is available, dilute to intermediate concentration ~20-50 ng/uL.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Well Sort Order = Row
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq cDNA Synthesis for Illumina
Supplier = Illumina
Catalog Number = 20022654
Website =
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
Placement Pattern = Column
Destination Containers
96 well plate
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Total Samples = 0
Prep Input Amount (ng) = 20
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA per pool. The recommended input is 10 ng RNA per pool.
Thermal Cycler Program = RT
Total Samples = 0
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 1000
Recommended Prep Input (ng) = Each reaction requires 10-1000 ng of DNase-treated total RNA. If RNA is not limiting, the recommended input is 1000 ng RNA. High RNA input amounts are recommended for rare clones.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Total Samples = 0
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 10-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Total Samples = 0
Prep Input Amount (ng) = 1000
Recommended Prep Input (ng) = Each reaction requires 50-1000 ng of DNase-treated total RNA. If RNA is not limited, the recommended input is 1000 ng RNA
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Total Samples = 0
Options
Additional Options and Dropdown Items
5X AmpliSeq cDNA Reaction Mix (uL)
Numeric
Decimal Places Displayed = 1
10X AmpliSeq RT Enzyme Mix (uL)
Numeric
Decimal Places Displayed = 1
AmpliSeq ERCC RNA Spike-in Mix
Numeric
Default = No
AmpliSeq ERCC RNA Spike-in Mix (uL)
Numeric
Decimal Places Displayed = 2
AmpliSeq ERCC RNA Spike-in Mix Lot#
Numeric
Desired Concentration (ng/uL)
Numeric
Read Only
Directions
Multiline Text
Default = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Nuclease-free water (uL)
Numeric
Decimal Places Displayed = 1
Prep Input Amount (ng)
Numeric
Default = 2
Range = 2 To 1000
Prep Input Volume (uL)
Numeric
Decimal Places Displayed = 2
Recommended Prep Input (ng)
Multiline Text
Read Only
Default = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
