Protocols and Configuration Slices

IPP Integration v2.4 provides protocols that contain configuration slices. These configuration slices are used to install other workflows and protocols.

QC_Protocols configuration component contains the qc-protocols base slice. This configuration does not contain any workflows, but it does provide the following protocols that are used by other workflows:

• DNA Initial QC
• Library Validation QC
• RNA Initial QC

The following table shows the components that are installed with the QC_Protocols configuration.

Components Installed with QC_Protocols

Component

Items Installed

Protocols
• DNA Initial QC 5.1.1
• Library Validation QC 5.1.1
• RNA Initial QC 5.1

Master Steps
• Add Multiple Reagents
• Adenylate ends & Ligate Adapters (TruSeq DNA) 5.1
• Pool Samples
• Aggregate QC (DNA) 5.1.1
• Aggregate QC (Library Validation) 5.1.1
• Aggregate QC (RNA) 5.1
• Bioanalyzer QC (DNA) 5.1.1
• Bioanalyzer QC (RNA) 5.1
• CaliperGX QC 5.1
• NanoDrop QC (DNA) 5.1
• NanoDrop QC (RNA) 5.1
• PicoGreen QC (DNA) 5.1
• PicoGreen QC (RNA) 5.1
• Qubit QC (DNA) 5.1
• Qubit QC (RNA) 5.1
• Tapestation QC (DNA) 5.1
• Tapestation QC (RNA) 5.1
• qPCR QC 5.1

Container types
• 384 well plate
• 96 well plate
• BioAnalyzer DNA 1000 Chip
• BioAnalyzer DNA High Sensitivity Chip
• BioAnalyzer RNA Nano Chip
• BioAnalyzer RNA Pico Chip
• Tube

Label groups/reagent categories
• TruSeq Custom Amplicon Adapters (A7-A5)
• TruSeq DNA LT Adapters (AD series)
• TruSeq Stranded mRNA LT Adapters (AR series)
• TruSeq HT Adapters (D7-D5)
• Nextera Enrichment & Rapid Capture Adapters (N7-E5)
• Nextera DNA Adapters (N7-N5, S7-S5)
• NoIndex
• TruSeq Small RNA Adapters (RPI series)

Reagent kits
• TruSeq DNA PCR-Free Kit - Adapter Plate Box
• TruSeq DNA PCR-Free Kit - Core Reagents Box
• TruSeq DNA PCR-Free Kit - SP Beads Box

Controls
• Endogenous Positive Control
• Exogenous Positive Control
• No Amplification Control
• No Reverse Transcriptase Control
• No Template Control
• PhiX v3

Sample custom fields
• Application
• Pooling
• Progress
• Reference Genome
• Sample Buffer
• Sample Conc.
• Units
• Volume (µl)
• Read Length
• Sample Type
• Sequencing Coverage
• Sequencing Method

Container custom fields
• Container Name
• LIMS ID (Container)
• Well

Project custom fields
• Project Name

Derived sample custom fields
• A260/280 ratio
• Conc. Units
• Concentration
• Sample Name
• Waiting
• Workflow

Measurement custom fields
• 28s/18s ratio
• A260
• A260/230 ratio
• A260/280 ratio
• BA Sample Name
• Conc. Units
• Concentration
• MW Units
• Molarity Units
• Number of Peaks found
• Number of Regions found
• Peak 1% Integrated Area
• Peak 1 Conc.
• Peak 1 MW
• Peak 1 Molarity
• Peak 1 Size - bp
• Peak 2% Integrated Area
• Peak 2 Conc.
• Peak 2 MW
• Peak 2 Molarity
• Peak 2 Size - bp
• Peak 3% Integrated Area
• Peak 3 Conc.
• Peak 3 MW
• Peak 3 Molarity
• Peak 3 Size - bp
• Peak 4% Integrated Area
• Peak 4 Conc.
• Peak 4 MW
• Peak 4 Molarity
• Peak 4 Size - bp
• Peak 5% Integrated Area
• Peak 5 Conc.
• Peak 5 MW
• Peak 5 Molarity
• Peak 5 Size - bp
• RIN
• RNA Area
• Region 1% of Total
• Region 1 Average Size - bp
• Region 1 Conc.
• Region 1 Molarity
• Region 2% of Total
• Region 2 Average Size - bp
• Region 2 Conc.
• Region 2 Molarity
• Region 3% of Total
• Region 3 Average Size - bp
• Region 3 Conc.
• Region 3 Molarity
• Region 4% of Total
• Region 4 Average Size - bp
• Region 4 Conc.
• Region 4 Molarity
• Region 5% of Total
• Region 5 Average Size - bp
• Region 5 Conc.
• Region 5 Molarity
• Sample Comment
• Size (bp)

The following table shows the AmpliSeq_for_Illumina_Protocols configuration slices and the workflows that are installed with IPP Integration v2.4.

AmpliSeq_for_Illumina_Protocols Configuration Slices and Workflows

Configuration Slice

Workflows

AmpliSeq-Illumina-BRCA-Panel-v1.0
• Equalizer AmpliSeq for Illumina BRCA Panel v1.0
• Library Prep AmpliSeq for Illumina BRCA Panel v1.0
• Standard Workflow AmpliSeq for Illumina BRCA Panel v1.0

AmpliSeq-Illumina-Cancer-HotSpot-Panel-V2-v1.0
• Library Prep AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.0
• Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.0

AmpliSeq-Illumina-Childhood-Cancer-Panel-v1.0
• DNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.0
• Equalizer AmpliSeq for Illumina Childhood Cancer Panel v1.0
• RNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.0
• Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.0

AmpliSeq-Illumina-Comprehensive-Cancer-Panel-v1.0
• Equalizer AmpliSeq for Illumina Comprehensive Cancer Panel v1.0
• Library Prep AmpliSeq for Illumina Comprehensive Cancer Panel v1.0
• Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.0

AmpliSeq-Illumina-Comprehensive-Panel-v3-v1.0
• DNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.0
• Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.0
• RNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.0
• Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.0

AmpliSeq-Illumina-Custom-DNA-Panel-v1.0
• Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.0
• Library Prep AmpliSeq for Illumina Custom DNA Panel v1.0
• Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.0

AmpliSeq-Illumina-Focus-Panel-v1.0
• DNA Library Prep AmpliSeq for Illumina Focus Panel v1.0
• Equalizer AmpliSeq for Illumina Focus Panel v1.0
• RNA Library Prep AmpliSeq for Focus Panel v1.0
• Standard Workflow AmpliSeq for Illumina Focus Panel v1.0

AmpliSeq-Illumina-Immune-Repertoire-Panel-v1.0
• Equalizer AmpliSeq for Illumina Immune Repertoire Panel v1.0
• RNA Library Prep AmpliSeq for Illumina Immune Repertoire Panel v1.0
• Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.0

AmpliSeq-Illumina-Immune-Response-Panel-v1.0
• Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.0
• RNA Library Prep AmpliSeq for Illumina Immune Response Panel v1.0
• Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.0

AmpliSeq-Illumina-Myeloid-Panel-v1.0
• DNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.0
• Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.0
• RNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.0
• Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.0

AmpliSeq-Illumina-TCR-beta-SR-Panel-v1.0
• DNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.0
• RNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.0

AmpliSeq-Illumina-Transcriptome-Human-Gene-Expression-Panel-v1.0
• Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.0
• RNA Library Prep AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.0
• Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.0

The following table shows additional configuration slices and workflows that are installed with IPP Integration v2.4.

Additional Configuration Slices and Workflows

Configuration Slice

Workflows

Covid
• CDC COVID-19 RT PCR v1.0
– Qiagen EZ1 Advanced XL CDC COVID-19 RT-PCR v1.0
– Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR v1.0
– Roche MagNA Pure 96 CDC COVID-19 RT-PCR v1.0
– Roche MagNA Pure Compact CDC COVID-19 RT-PCR v1.0
– Roche MagNA Pure LC CDC COVID-19 RT-PCR v1.0
– Sort Specimens to Extraction CDC COVID-19 RT-PCR v1.0
– bioMerieux EMAG Instrument CDC COVID-19 RT-PCR v1.0
– bioMerieux NucliSENS easyMAG Instrument CDC COVID-19 RT-PCR v1.0
• Illumina COVIDSeq Workflow v1.3
• Respiratory Virus Panel v1.0

DNA_Protocols
• Illumina DNA PCR-Free Library Prep Manual v1.0.2
• Illumina DNA Prep (M) Tagmentation v1.0.4
• Nextera Mate Pair v1.0.5
• Nextera XT DNA v2.0.5
• TruSeq DNA PCR-Free v2.0.5
• TruSeq Nano DNA v1.0.5
• TruSight Whole Genome Workflow v1.0

IGA
• Illumina Genomics Architecture - Library Prep Automated v2.0
– Sample Selection (IGA v2.0)
– Sample Plating (IGA v2.0)
– Blood Extraction (IGA v2.0)
– Saliva Extraction (IGA v2.0)
– Illumina DNA PCR-Free (IGA v2.0)
– Illumina DNA with Enrichment (IGA v2.0)
– Sequencing Platform Selection (IGA v2.0)
• Illumina Genomics Architecture - NovaSeq Sequencing v2.0
– Run Format (IGA v2.0)
– NovaSeq Standard (IGA v2.0)
– NovaSeq Xp (IGA v2.0)
– AUTOMATED - NovaSeq Run (IGA v2.0)

IGA workflows require additional installation steps. For assistance, contact Illumina Technical Support. Note also that Illumina Genomics Architecture - NovaSeq Sequencing v2.0 workflow is not the same workflow as NovaSeq 6000 v3.5.

Infinium_Array
• GenomeStudio v1.0
• ILASS Infinium Genotyping Assay v1.0
• ILASS Infinium Genotyping with PGx v1.0
• Infinium HD Methylation Assay Manual v1.1
• Infinium HTS Assay Manual v1.1
• Infinium LCG Assay Manual v1.1
• Infinium XT Assay Manual v1.1

Methylation_Protocols
• TruSeq ChIP-Seq v1.0.5
• TruSeq Methyl Capture EPIC v2.0.6

RNA_Protocols
• Illumina Stranded mRNA Prep Ligation v1.0
• Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.0
• TruSeq Small RNA v1.0.5
• TruSeq Stranded mRNA v2.1.5

Targeted_Amplicon_Protocols
• TruSeq Custom Amplicon v1.0.5

Targeted_Enrichment_Protocols
• Illumina DNA Prep with Enrichment (S) Tagmentation v1.1
• Illumina RNA Prep with Enrichment (L) Tagmentation v1.0
• Nextera Rapid Capture Custom Enrichment v2.0.6
• TruSeq DNA Exome v2.0.5
• TruSeq RNA
– TruSeq RNA Access v2.0.5
– TruSeq RNA Exome v1.0.3

TruSight_Oncology_Protocols
• TruSight Oncology 500 ctDNA v1.0
• TruSight Oncology 500 HT v1.0
• TruSight Oncology 500 v1.0
• TruSight Tumor 170 v2.0.5