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Integrating multiomics into biological research provides scientists with novel scientific insights that make groundbreaking new discoveries possible. M-AMR-00368

Table of Contents Click on each below to explore a topic What is multiomics? Why multiomics? Popular multiomics combinations Multimodal approaches in multiomics What does a multiomics workflow look like? Most frequently used multiomics workflows Genomics and transcriptomics workflows for bulk-cell analysis Epigenetics/transcriptomics/proteomics workflow for bulk-cell analysis Methylation and genotyping array workflows Single-cell analysis workflows Spatial analysis workflow Single-cell analysis workflow combining ATAC-Seq with mRNA sequencing The time to get started is now M-AMR-00368

What is multiomics? Multiomics explores multiple omes — combinations of the genome, proteome, transcriptome, and epigenome — in one experiment. Proteomics explores protein expression to understand cellular phenotypes and function. Transcriptomics studies the complete set of RNA transcripts produced by a genome. Epigenetics looks at how cells control gene activity through processes like DNA methylation. Genomics focuses on the structure, function, evolution, mapping and editing of information in an organism’s DNA. Figure 1: Individual omes can be studied in combination. M-AMR-00368

Why multiomics? Biological regulation is complex and phenotypes are influenced by a myriad of factors that extend beyond DNA. An unbiased characterization of the cellular and environmental factors that influence genotypes and phenotypes is necessary to comprehensively understand novel systems. Integration of multiomics accelerates: • Discovery of novel associations between biological entities • Identification of relevant biomarkers • Development of effective therapies A multiomics approach increases our understanding Pejman Mohammadi, PhD of biology by helping you us see things that would be hidden with one type of data. If something is happening Associate Professor of at the metabolism level, you’re going to miss it if you’re Computational Biology, just looking at the transcriptome. Scripps Research Institute, La Jolla M-AMR-00368

Popular multiomics combinations Multiomics Implications combination Genotypes can offer information on susceptibility to diseases. Incorporating RNA Genomics + sequencing helps researchers measure the functional consequences of genetic transcriptomics variation and may reveal therapeutically exploitable expression patterns. Genomics + This multiomic approach connects a genotype to the phenotype for more informed proteomics research into a disease state. Transcriptomics + RNA sequencing interrogates gene expression patterns that differentiate cells proteomics or distinct cell populations. Incorporating protein detection can link cell-specific expression with protein biomarkers. Genomics + epigenomics Combining epigenomic findings with genetic information allows researchers to understand patterns of gene regulation and how they connect with the genotypes Transcriptomics + underlying diseases. epigenomics Combining epigenomics and transcriptomics allows researchers to directly measure the ties between gene regulation and gene expression. Danny Wells, PhD Single omics can be useful for straightforward questions, but in topics like immunotherapy-resistant cancer, you Scientific Co-Founder and want to have as much information as possible. That’s Senior Vice President of where multiomics really shines. Strategic Research, Immunai M-AMR-00368

Multimodal approaches in multiomics Multiomics allows you to explore different modalities (data types such as DNA, RNA, and protein) simultaneously by leveraging three main experimental approaches: bulk-cell analysis, single-cell analysis, and spatial analysis. • Bulk-cell analysis: Analyzes pooled cell Starting material populations, tissue sections, or biopsies in bulk for greater efficiency. Method Bulk-cell analysis Spatial Single-cell analysis analysis • Single-cell analysis: Generates a high- resolution, multiomic understanding Expected data of individual cells and their functions, interactions, and dynamic behavioral events. Average of Average of all Different cell types all cells cells in an area and characteristics • Spatial analysis (aka spatial genomics): A new frontier in molecular biology that captures the genomic information of single cells within their native tissue environment. There are a variety of insights we’ve gained using a Ben Humphreys, MD, PhD multiomics approach that we wouldn’t have if we had just used a single modality. Chief of the Division of Nephrology at Washington University, St. Louis M-AMR-00368

What does a multiomics workflow look like? Although the details differ depending on A library is a collection of similarly sized nucleic the omes you want to explore, multiomics acid fragments with known adapter DNA workflows generally start with nucleic acid sequences added to the 5ʹ and 3ʹ ends. Sample isolation from which nucleic acid libraries or preparation enables sample compatibility with samples are then prepared. Illumina sequencers and arrays. Following this, data readouts are collected and then analyzed. Nucleic acid Sample or Sequencing Data isolation library prep or arrays analysis Minoli Perera, PharmD, PhD Multiomics increases our understanding of biological mechanisms…which may lead to the discovery of Associate Professor new drug targets that may prevent adverse events in Northwestern University specific populations. Feinberg School of Medicine M-AMR-00368

Most frequently used multiomics workflows Genomics and transcriptomics workflows for bulk-cell analysis Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment Illumina DNA DRAGEN™ Germline PCR-Free Prep Genomics Whole- NovaSeq™ 6000 System + genome- Illumina DNA Prep NovaSeq v1.5 Reagents sequencing (for FFPE Samples) DRAGEN Somatic (Cancer Research) Bulk-cell Whole-exome- Illumina DNA Prep DRAGEN sequencing with Enrichment Enrichment Trancriptomics Whole- Illumina Stranded NovaSeq 6000 System + DRAGEN RNA BaseSpace™ transcriptome- Total RNA Prep NovaSeq v1.5 Reagents Correlation DRAGEN sequencing with Ribo-Zero Plus NextSeq 2000 System Differential Engine Expression + Reagents M-AMR-00368 Illumina Stranded DRAGEN RNA mRNA Prep mRNA sequencing Illumina RNA Prep with Enrichment (for FFPE samples) DRAGEN Differential Expression For Research Use Only. Not for use in diagnostics procedures.

Epigenetics/transcriptomics/proteomics workflow for bulk-cell analysis* Assay for transposable-accessible chromatin with sequencing (ATAC-Seq) and bulk epitope and nucleid acid sequencing (BEN-Seq) workflows. Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment Epigenomics ATAC-Seq Illumina Tagment DNA Open source tools BaseSpace TDE1 Enzyme and Bowtie 2 Correlation Engine Buffer Kits Burrows-Wheeler Alignment Tool Bulk-cell TotalSeq™ -A Reagents NovaSeq 6000 System + NovaSeq v1.5 Reagents Transcriptomics + proteomics NextSeq 2000 System + Reagents BEN-Seq Illumina Stranded Open source tools DESeq2 mRNA Prep Illumina RNA Prep with Enrichment (for FFPE samples) M-AMR-00368 For Research Use Only. Not for use in diagnostics procedures.

Methylation and genotyping array workflows Arrays enable quantitative interrogation of selected methylation sites across the epigenome or variants across the genome. Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment Methylation Infinium™ array MethylationEPIC Kit Bulk-cell (human samples) Infinium Mouse Methylation Array (murine samples) GenomeStudio™ Bioconductor Software Tools iScan™ System Genotyping Infinium Global array Diversity Array-8 Kit (high throughput for human samples) Infinium Global Screening Array-24 Kit (high throughput for human samples) For Research Use Only. Not for use in diagnostics procedures. M-AMR-00368

Single-cell analysis workflows* Cellular indexing of transcriptomes and epitopes with sequencing (CITE-Seq) and proteogenomics Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment TotalSeq –A, B or C Reagents Multiomics Analysis Software (MAS) SeqGeq Software Single-cell CITE-Seq BD AbSeq Assay NovaSeq 6000 System + Transcriptomics Single Cell Immune Profiling NovaSeq v1.5 Reagents + proteomics NextSeq 2000 System + Reagents Single Cell Gene Expression CellRanger Software Genomics Proteo- TotalSeq - D Reagents Tapestri Pipeline Tapestri Insights + proteomics genomics Tapestri Platform Tapestri Single-Cell Panels NextSeq 2000 System + Reagents M-AMR-00368 For Research Use Only. Not for use in diagnostics procedures.

Spatial analysis workflow* Cellular indexing of transcriptomes and epitopes with sequencing (CITE-Seq) Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment Spatial CITE-Seq Visium Spatial Gene Visium Spatial Expression. Gene Expression Transcriptomics NovaSeq 6000 System + + proteomics GeoMx® Digital NovaSeq v1.5 Reagents GeoMx –Spatial Biology Spatial Profiler NextSeq 2000 System Data Analysis GeoMx RNA Assays GeoMx Protein Assays + Reagents Single-cell analysis workflow combining ATAC-Seq with mRNA sequencing* Click on underlined text to explore Library prep Sequencing Secondary analysis Tertiary analysis reagents and equipment Single-cell ATAC-Seq + Open source tools Open source tool Epigenomics mRNA-Seq Bowtie 2 Seurat by the Satija + transcriptomics Burrows-Wheeler Lab at New York Alignment Tool Genome Center Chromium Single NovaSeq 6000 System + DRAGEN Cell Multiome ATAC NovaSeq v1.5 Reagents Single-Cell RNA + Gene Expression NextSeq 2000 System + Reagents 10X Genomics Cell Ranger/Loupe Browser For Research Use Only. Not for use in diagnostics procedures. M-AMR-00368

Workflow Key *Some multiomics workflows use both Illumina products and external partner products DNA library prep (Illumina) RNA library prep (Illumina) Sequencing/array instrument/reagents (Illumina) Secondary analysis software (Illumina) Tertiary analysis software (Illumina) Proteomics Non-Illumina products Non-Illumina secondary analysis software Non-Illumina tertiary analysis software M-AMR-00368

The time to get started is now Here’s why you should partner with Illumina. Our multiomics reagents, equipment and protocols have been validated with hundreds of publications in high-impact, peer-reviewed journals. (pubmed.ncbi.nlm.nih.gov/?term=illumina+sequencing) Illumina technology has the broadest range of applications to enable multiomic analyses on one device and is built to support emerging changes in the multiomics landscape. Illumina supports over 10,000 labs across 115 countries. 24/7 technical support professionals are ready to help you with any project. Need a crash-course on a topic? We have an extensive library of free online training resources to support your research. (support.illumina.com/training.html) M-AMR-00368

Learn more about the power of multiomics Download our free ebook: illumina.com/more-with-multiomics5 1. Cell Biologist Market Research. Percepta Associates, Inc. perceptaassociates.com. Accessed 2021. 1.800.809.4566 toll-free (US) | +1.858.202.4566 tel [email protected] | www.illumina.com © 2021 Illumina, Inc. All rights reserved. All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, see www.illumina.com/company/legal.html. M-AMR-00368 v1.0