March 2025

Powerful, intuitive, scalable multiomics analysis

Illumina Connected Multiomics (ICM), the newest addition to the Illumina Connected Software portfolio, is designed to streamline data integration, visualization, and interpretation. ICM enables integration of layers of omic data, providing a multidimensional view of cellular function, allowing for simultaneous investigation of the data. It empowers researchers to overcome challenges related to data complexity, scalability, and storage.

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Are you dreaming of a user-friendly NGS data analysis tool that doesn’t require advanced bioinformatic skills?

Partek™ Flow™ is a comprehensive start-to-finish bioinformatics data analysis solution for next-generation sequencing applications. Across a wide range of data and application types, it provides a user-friendly experience, allowing all researchers to analyze data and take on their analysis journey at their own pace and skill level.

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Depending on your experimental setup, you may want to choose a “reading” vs. “counting” application. Do you know how they differ?

For novice users of next-generation sequencing, the jargon can be confusing. Robert Yamulla provides a simple explanation of the difference between reading and counting applications and use cases for which one is more suitable than the other.

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Innovations to enable multiomics

1

Dual insights. One easy assay. Illumina 5-base solution for methylation and variant detection

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Dual insights. One easy assay. Illumina 5-base solution for methylation and variant detection

Introducing a revolutionary solution to measure DNA methylation and genetic variation together, with exceptional accuracy, simplicity, and scale. Novel base conversion chemistry and powerful algorithms enable simultaneous genomic and epigenomic discovery in a single readout.

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2

Illumina unveils spatial transcriptomics technology 

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Illumina unveils spatial transcriptomics technology 

Planned for commercial release in 2026, Illumina spatial technology will be a unique end-to-end spatial transcriptomics solution for use with Illumina high-throughput sequencing systems. This solution will allow researchers to examine the spatial proximity of millions of cells per experiment, enabled by a capture area nine times larger than existing technologies, and with four times greater resolution.

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Multiomics in action

Publication highlights from the research community

Proteomics

Multiomics

Single-cell

Plasma proteome variation and its genetic determinants in children and adolescents

Published by Matthias Mann’s group, this study is one of the most comprehensive pQTL analyses in pediatric populations to date. Using a mass spec (MS)-based approach in plasma from over 2,100 children, the results showed 1,216 proteins, with one-third regulated by genetic variation, highlighting the persistence of these genetic effects into adulthood and underscoring the potential of protein QTLs. Furthermore, the study demonstrates the complementarity of MS-based and affinity-based proteomics methods to refine our understanding of protein variation and its genetic determinants. 

Learn more about the NGS-based Illumina Protein Prep solution

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Proteomics

Multiomics

Single-cell

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

In this study, the authors investigate the role of the transcription factor PROX1 in maintaining hepatocyte identity and preventing liver cancer. The research employs multiomic strategies, including transcriptomic (bulk and single-cell), epigenomic (ATAC-seq) and proteomic (mass spectrometry) analyses, to investigate the role of safeguard repressors in regulating cell fate and plasticity across 18 cell types. The findings suggest that PROX1 actively suppresses cell fate plasticity to maintain lineage identity and prevent disease.

Visit our Multiomics content hub for additional resources 

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Proteomics

Multiomics

Single-cell

Multiomic profiling of T cell lymphoma after therapy with anti-BCMA CAR T cells and GPRC5D-directed bispecific antibody

Using a multiomic approach, research groups in Leipzig and Cologne highlight the evolution of a CAR-carrying peripheral T cell lymphoma following CAR T cell and bispecific T cell engager therapy. Despite their success, CAR T therapies come with notable risks, including the potential for developing secondary malignancies following therapy. Through spatially resolved multiomic single-cell dissection, the authors reveal critical insights that can arise as post-CAR T complications. 

Learn more about Illumina Single Cell 3’ RNA Prep

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Educational resources ​to learn more

On Demand Webinar
More single-cell data, less equipment
On Demand Webinar
More single-cell data, less equipment 
Compatible with any Illumina sequencer, Illumina Single-Cell 3’ RNA Prep leverages emulsion-based Pre-templated Instant Partitions (PIPs) to enable profiling of hundreds to millions of cells, eliminating microfluidics and minimizing instrumentation requirements.​
eBook
Liquid Biopsy in Cancer Research
eBook
Liquid Biopsy in Cancer Research
This educational eBook describes next-generation sequencing (NGS) applications for incorporating a multiomic approach.  Workflows are outlined for detailed profiling of multiple analytes present in blood, including cell-free RNA (cfRNA) sequencing, single-cell sequencing of circulating tumor cells (CTCs) and more.
Webinar
Innovations to drive the multiomics revolution
Webinar
Innovations to drive the multiomics revolution
Early access collaborators join Illumina R&D to present Spatial transcriptomics, Illumina Connected Multiomics data analysis, constellation mapped reads and Illumina 5-base solution for epigenetics.