Discover Single Cell Biology at Scale

Our single cell sequencing technology enables scalable sample indexing, cell throughput, and multi-omics analysis

OUR Technology

How it works

ScaleBio’s single cell sequencing library preparation technology and single-cell analysis solutions enable unprecedented sample multiplexing, cell throughput, and multi-omics profiling of cells across a broad range of genomic, epigenomic, transcriptomic, proteogenomic, and multi-omic applications.

Split-pool barcoding and combinatorial indexing methods leverage the cell as a compartment for a simple, instrument-free single-cell workflow as follows:

1. Permeabilized cells are distributed in a multi-well plate where barcoded probes tag cellular analytes with a barcode that is uniform for all cells within a single well.

2. These barcoded cells are pooled, then randomly re-distributed for another round of barcoding.

3. This process is completed when the desired barcode space has been achieved. The number of cells profiled can be scaled up exponentially with repeated rounds of pooling and splitting to enable single cell experiments with hundreds of thousands to millions of cells.


ScaleBio's products enable a unique combination of increased throughput, multi-omics support, cost-effective library preparation, and high-quality data.

Scalable sample indexing
Scalable sample indexing

Enables higher levels of sample multiplexing per experiment with ability to store sample for future experiments

Highly efficient chemistries
Highly efficient chemistries

Enables the generation of complex single cell libraries for deeper profiling of cells

Scalable cell throughput
Scalable cell throughput

Enables profiling of hundreds of thousands to millions of cells per experiment

Low library preparation costs
Cost effective library preparation

Enables large and complex library generation at low cost per sample and cell

Multi-modal application support
Multi-modal application support

Enables Genomic, Proteomic, Epigenomic, Transcriptomic and Multi-omics applications

Instrument agnostic and compatible
Instrument agnostic and compatible

Compatible with and independent of on-market single cell droplet and well based systems

Watch how ScaleBio's technology and methods have been used in single cell analysis of mammalian organogenesis


ScaleBio’s library preparation technology enables the generation of larger and more complex single cell libraries, leading to improved visualization and increased insights from high-dimensional single-cell data.

about our technology

Single-Cell Profiling and Analysis


ScaleBio’s single-cell chromatin accessibility kit enables users to profile up to 300,000 nuclei in a single experiment, decreasing the cost per cell while maintaining data quality. The streamlined workflow integrates tagmentation and sample indexing, enabling users to profile up to 24 samples simultaneously. Please contact us below for more information or to request a quote.



ScaleBio is quickly following-on with additional single-cell combinatorial indexing applications and workflows, including single-cell transcriptome profiling for higher throughput experiments. Our scRNA kit will enable the price point needed for rigorous perturbation studies, large patient cohorts, and more.

If interested in participating in our RNA early access programs or learning more about planned applications for high-parameter protein and methylation profiling solutions, please reach out below.

Want to try out our technology?

Explore our available opportunities

Join us in unlocking the potential for single cell analysis in biological discovery.

Companies don't do great science, people do. ScaleBio has patented technology, a strong co-founding team, leading scientific advisors, and value-add investors with a proven track record in building successful life sciences technology companies.

We are building a diverse, multi-disciplinary team of scientists, engineers, technologists, and bioinformaticians that share a passion for unlocking the potential of single cell sequencing. Are you interested in joining us?


Publications and Resources

Representative publications citing single cell split-pool barcoding and combinatorial indexing methods.


Comprehensive single-cell transcriptional profiling of a multicellular organism

SCIENCE 357, 6352 (2017)

High-content single-cell combinatorial indexing


Massively multiplex chemical transcriptomics at single-cell resolution

SCIENCE 367, 6473 (2020)

Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis

Commun Biol 3, 213 (2020).


Scientific Co-Founders

ScaleBio was founded by a multidisciplinary team of scientists and technologists, with expertise in next generation sequencing, genomics and proteomics and bioinformatics, that share a mission for unlocking the potential of single cell analysis at scale.

Sean Scott@2x
Sean Scott

Life Sciences Technology

Frank Steemers@2x
Frank Steemers


Gary Nolan@2x
Garry Nolan


Jay Shendure@2x
Jay Shendure


Cole Trapnell@2x
Cole Trapnell


Contact Us

Get in touch for more information about our technology or products.

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