Single Cell Methylation at Scale. Finally.

Our new Single Cell Methylation Kit gives you an unprecedented ability to transform your understanding of biology. With both scalability and highly sensitive chemistry, you'll get a revolutionary view into cellular heterogeneity.



As the first ever commercial solution for single-cell resolution into methylation states, our Single Cell Methylation Kit allows you to profile single-cell methylation states across tens of thousands of cells. You can now fix your samples with the utmost flexibility in sample collection, storage, and transport-allowing you to process your samples on your own time. The streamlined workflow and powerful chemistry enable the analysis of tens of thousands of cells in a single run. Paired with our easy-to-use data analysis pipeline, you can achieve results quickly and efficiently.



Up to 18,000 cells per run


>70% mapping rates


Fixation-compatible for sample storage, transport, and batching

Target Enrichment Compatible

Reduce sequencing costs while conserving meaningful biological data

Single Cell Methylation Kit Workflow Overview

Our single-cell methylation workflow begins with fixed nuclei. Nuclei samples are barcoded upfront in tagmentation, enabling sample multiplexing. 24 nuclei are deposited per well, and then distributed across a 96-well plates to profile >18,000 single cell methylomes in a single run. Bisulfite conversion is then performed, followed by cleanup and the addition of adaptors. Finally, a second barcode is added across plates to complete library construction.

Using the ScaleBio Seq Suite, libraries are then sequenced and data is processed to produce a single-cell methylation matrix. The workflow provides many convenient stopping points and can be performed without any additional instrumentation using common lab equipment.


High Data Quality on Diverse Sample Types

The ScaleBio Single Cell Methylation Kit workflow demonstrates robust performance across different tissue types, sample formats and species.

When comparing human and mouse unique reads to total reads, a similar amount of library complexity is observed in both species across several experiments, performed over the course of three months.

Ratio of Unique Reads vs. Total Reads

human mouse unique vs. total

The Single Cell Methylation Kit displays comparable CpG coverage for both human and mouse samples across several experiments, performed over the course of three months.

Ratio of CpG Coverage vs. Unique Reads

Cpg vs Unique

Across a wide variety of cell and tissue types, similar ratios of median unique reads to median total reads are observed, indicating uniform performance of the library preparation chemistry.

Ratio of Unique Reads vs. Total Reads

unique vs. total many samples

Frequently asked questions

We currently offer this workflow as a Service.  You can inquire about your project and discuss pricing by visiting our Services page.

Nuclei from primary tissues in fresh dissociated, snap-frozen, and OCT-embedded formats have been demonstrated in addition to PBMCs and cell lines.

Freshly fixed samples can be stored in the freezer for up to a week. Tagmented nuclei can be stored in the freezer for up to 6 months.

A single cell methylation analysis pipeline is provided with the product to take you from raw sequencing outputs to a cell-methylation state matrix. 

We have tested compatibility on MiSeq, iSeq, NextSeq 500/550, NextSeq 1000/2000, NovaSeq6000.


Want to learn more?


Featured publications View All

High-throughput robust single-cell DNA methylation profiling with sciMETv2

Nature Communications (2022)


Want to learn more about the Single Cell Methylation Kit?

Our Methylation workflow is currently available through our Services product offering.  Please refer to Services for more details.

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