Multiomic Sequencing Methods

Simplifying the approach to multiomics

Deciding on the ideal multiomics approach for your next experiment can be a daunting task. Our table is designed to guide you in selecting the most suitable omics solutions for your needs. Explore benefits and solutions to discover how multimodal techniques, such as bulk sequencing, single-cell, spatial sequencing methods, and more, can significantly improve the breadth of your next multiomic studies to provide a better understanding of biology.

Bulk sequencing

Bulk sequencing refers to an approach that pools cell populations, tissues, and other samples to arrive an average measurement. This method is useful for a wider breadth of analysis that is also cost effective when evaluating differences between samples.

Genomics

	Key Benefit	Library Prep	System(s)	Informatics
Genomics
Whole-Genome Sequencing	See the entire genome	Illumina DNA PCR-Free Prep Illumina DNA Prep with Enrichment	NovaSeq 6000 NovaSeq X Series	DRAGEN Germline DRAGEN Somatic (Cancer Research) BaseSpace Correlation Engine
Exome Sequencing	Detect exonic variants	Illumina DNA Prep with Enrichment	NovaSeq 6000 NovaSeq X Series NextSeq 2000	DRAGEN Enrichment DRAGEN CNV Caller BaseSpace Correlation Engine

Epigenetics

	Key Benefit	Library Prep	System(s)	Informatics
Epigenetics
Methylation Sequencing	Explore the methylome	TruSeq Methyl Capture EPIC	NovaSeq 6000 NovaSeq X Series NextSeq 2000	DRAGEN Methylation App
ChIP-Seq	Understand gene regulation	TruSeq ChIP	NovaSeq 6000 NovaSeq X Series	BaseSpace ChIPSeq App
ATAC-Seq	Map chromatin accessibility across the genome	Illumina Tagment DNA TDE1 Enzyme and Buffer Kits	NovaSeq 6000 NovaSeq X Series NextSeq 2000	Open Source Tools: Bowtie 2

Transcriptomics

	Key Benefit	Library Prep	System(s)	Informatics
Transcriptomics
Total RNA-Seq	Get full transcriptome data	Illumina Stranded Total RNA Prep with Ribo-Zero Plus	NovaSeq 6000 NovaSeq X Series NextSeq 2000	DRAGEN RNA DRAGEN Differential Expression BaseSpace Correlation Engine
mRNA-Seq	View the coding transcriptome	Illumina Stranded mRNA Prep Illumina RNA Prep with Enrichment (for FFPE samples)	NovaSeq 6000 NovaSeq X Series NextSeq 2000	DRAGEN RNA DRAGEN Differential Expression BaseSpace Correlation Engine

Transcriptomics

	Key Benefit	Library Prep	System(s)	Informatics
Proteomics
NGS-based proteomics	Identify protein quantification levels with a wide discovery panel	Illumina Protein Prep	NovaSeq 6000 NovaSeq X Series	DRAGEN Protein Quantification Illumina Connected Multiomics

Transcriptomics + Proteomics

	Key Benefit	Library Prep	System(s)	Informatics
Transcriptomics + Proteomics
BEN-Seq	Get gene expression and surface protein expression profiles simultaneously	Illumina Stranded mRNA Prep Illumina RNA Prep with Enrichment (for FFPE samples) Antibodies can be sourced from BioLegend	NovaSeq 6000 NovaSeq X Series NextSeq 2000	Open Source Tools: DESeq2

Liquid Biopsy

	Key Benefit	Library Prep	System(s)	Informatics
Liquid Biopsy
ctDNA Sequencing	Noninvasive approach detecting ctDNA in plasma from solid tumors	TruSight Oncology 500 ctDNA	NovaSeq 6000 NovaSeq X Series	DRAGEN and Pierian Clinical Genomics Workspace Software

Solid Tumor

	Key Benefit	Library Prep	System(s)	Informatics
Solid Tumor
Targeted Cancer Screening	Identify all mutational classes and IO biomarkers in a single assay	TruSight Oncology 500 High-Throughput	NovaSeq 6000 NovaSeq X Series	DRAGEN and Pierian Clinical Genomics Workspace Software

Single-cell sequencing

Single-cell sequencing is an advanced method that allows analysis of omic sequences at the resolution of individual cells. Such an approach allows researchers to comprehensively evaluate heterogeneity of populations that otherwise might be missed in bulk sequencing studies.

RNA

		Key Benefit	Solution	Learn More
Transcriptomics
Single-Cell Sequencing	Illumina Single Cell 3’ RNA Prep	Accessible, highly-scalable single-cell technology by Illumina	Illumina Single Cell 3' RNA Prep is compatible with NovaSeq X, NovaSeq 6000, and NextSeq 1000 and 2000 Platforms. Data analysis is provided by DRAGEN, Partek, and Ilumina Connected Analytics.	Learn more
RNA	Single-Cell RNA-Seq	Reveal transcriptome cell-to-cell variation	Single-Cell RNA-Seq method is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with library prep and data analysis provided by 10X Genomics or through the Illumina DRAGEN Single Cell BaseSpace App.	Learn More at 10X

Epigenetics

		Key Benefit	Solution	Learn More
Epigenetics
Epigenetics	Single-Cell ATAC-Seq	Access chomatin accessibility patterns to view cell-to-cell variation	Single-Cell ATAC-Seq method is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with library prep and data analysis provided by 10X Genomics and open source tools such as Bowtie 2 and Seurat by the Satija Lab.	Learn More at 10X
RNA + Epigenetics	Single-Cell Gene Expression + ATAC-Seq	Correlate transcriptome and chomatin accessibility patterns at the single-cell level	Utilize the Multiome Single-Cell ATAC-Seq + gene expression prep kit from 10X genomic on the NovaSeq 6000 and NextSeq 2000 platforms.	Download Tech Note

RNA + Proteomics

		Key Benefit	Solution	Learn More
Proteomics
RNA + Proteomics	CITE-Seq	Evaluate gene expression and surface protein expression levels simultaneously at single-cell resolution	CITE-Seq is compatible with the NovaSeq 6000 and NextSeq 2000 platforms, with compatible antibodies from BD or BioLegend and single-cell prep kits from 10X Genomics. Analysis tools can also be found from 10x Genomics, BD or BioLegend.	Learn more about BioLegend solutions

DNA + Protein

		Key Benefit	Solution	Learn More
DNA + Protein	Proteomics	Correlate known tumor genomic variants to cell-surface proteins at single-cell resolution	The Mission Bio DNA + protein panel for tumor samples is compatible with the NextSeq 2000 platform, with compatible antibodies from BioLegend and the prep instrument, prep kit, and analysis tools from Mission Bio	Learn more about Mission Bio's Tapestri Platform

Spatial sequencing methods

Spatial sequencing methods offers a contextual view of cell activity and information as it combines omic information within intact tissues. This allows researchers to gain unprecedented insights to unravel the structure and function of complex tissues.

Spatial Methods

RNA

		Key Benefit	Solution	Learn More
RNA	RNA-Seq Spatial	Understand the gene expression patterns from a particular region of interest within FFPE or fresh frozen tissue sections	RNA-Seq spatial sequencing is compatible with NovaSeq 6000 and NextSeq 2000 Platforms, with library prep and data analysis provided by NanoString	Download Tech Note

RNA + Proteomics

		Key Benefit	Solution	Learn More
RNA + Proteomics	CITE-Seq Spatial	Correlate targeted gene expression and protein expressions patterns from FFPE or fresh frozen tissue sections	CITE-Seq Spatial sequencing is compatible with NovaSeq 6000 and NextSeq 2000 Platforms, with library prep and data analysis provided by NanoString	Learn more about Nanostring solutions

Multiomic Sequencing Methods

Multiomics methods

Explore a wide array of sequencing omic methods for multimodal applications

Simplifying the approach to multiomics

Bulk sequencing

Single-cell sequencing

Spatial sequencing methods

Spatial Methods

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MiSeq i100 Series

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MiSeq i100 Series

MiSeq i100 Series

MiSeq i100 Series

MiSeq i100 Series

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Multiomic Sequencing Methods

Multiomics methods

Explore a wide array of sequencing omic methods for multimodal applications

Simplifying the approach to multiomics

Bulk sequencing

Single-cell sequencing

Spatial sequencing methods

Spatial Methods