Learn how to sequence the epigenome AND transcriptome in single cells

Single Cell Multiomics is here, and it’s cheaper and easier than ever. Epigenomic and Transcriptomic methods are powerful tools alone, but combining them into one experiment, in single cells, can remove a ton of inference when interpreting data.  Here’s how:

  • Measuring the epigenome alone with a method like ATAC-Seq can show whether DNA is open, or closed, throughout the genome. And while a gene’s presence within open chromatin often means that gene switches and transcription factor binding sites are potentially active, expression may not always occur.
  • RNA-Seq alone shows patterns of what genes are actively transcribed and therefore expressed” not “what is expressed. But the mechanisms underlying those gene expression patterns may not be clear from RNA Data alone.

Combining RNA-Seq with ATAC-Seq allows for measurement of a major mechanism of gene regulation (chromatin state, ATAC-Seq), plus, direct profiling of whether a given chromatin state correlates with expression (RNA-Seq). This multiomic combination is particularly powerful at single-cell resolution, where it can reveal exciting discoveries in the complex regulatory interactions driving cell activity and differentiation pathways.


Illumina’s new Single Cell Multiomics Quickstart Guide reviews the most popular method for combining ATAC-Seq and Gene Expression Profiling in single cells.  Discover why 84% of epigenomics researchers also use transcriptomics, plus, over 145 publications that utilize single cell multiomic sequencing.

To learn more, download our NEW eBook on Single Cell Epigenomic and Transcriptomic Sequencing: https://www.illumina.com/destination/et-ebook.html


  • Percepta Associates, Inc. Global Multiomics Practices Final Report 2022.
  • Digital Science. Dimensions [Software] available from app.dimensions.ai. Accessed May 20, 2021, under license agreement.
  • Compared to the S4 flow cell on the NovaSeq 6000.

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