Discover Single Cell Biology at Scale

Our single-cell profiling and analysis solutions enable increased levels of sample indexing and cell throughput for larger, more complex studies.

OUR Technology

How it works

Our ScaleBio™ combinatorial indexing based single-cell profiling and analysis solutions enable increased levels of sample multiplexing, increased cell throughput, and support for a broad range of genomic, epigenomic, transcriptomic, proteogenomic, multi-omic applications.

Combinatorial indexing technology and methods leverage the cell as the compartment, enabling an accessible, instrument-free, 2-day single-cell (and nuclei) profiling workflow:

1. Permeabilized cells are distributed in a multi-well plate where barcoded probes tag cellular analytes with a barcode.

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

3. This process is completed when the desired barcode space has been achieved.

The number of cells or nuclei can be scaled up exponentially with repeated rounds of pooling and splitting, for single-cell experiments with up to 96 samples and 100s of thousands to millions of cells, all at a fraction of the cost of on-market single-cell isolation instruments.


ScaleBio single-cell profiling and analysis solutions enable a unique combination of increased throughput, multi-omics support, high data quality and lower overall prep and sequencing costs.

Scalable sample indexing
Scalable sample indexing

Enables sample multiplexing of up to 96 samples per experiment, with the ability to fix, store, and transport samples.

Highly efficient chemistries
Highly efficient chemistries

Enables the construction of complex single-cell libraries that result in exceptional data quality.

Scalable cell throughput
Scalable cell throughput

Enables profiling of hundreds of thousands to millions of cells or nuclei per experiment with low multiplet rates.

Low library preparation costs
Cost effective library preparation

Enables library construction at a fraction of the cost per sample and cell cost relative to on-market systems.

Multi-modal application support
Broad application support

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

Instrument agnostic and compatible
Accessible technology and workflow

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

Learn about ScaleBio technology and how it's workflow can empower researchers to complete sample to insight solutions.


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

ScaleBio Product Offerings


The ScaleBio Single Cell RNA Sequencing Kit and analysis software enable the indexing of up to 96 samples and up to 125,000 cells in a single experiment, supporting larger and more complex studies. Our kit is compatible with but not limited to: mouse and human cell lines, PBMCs, and samples types required the use of nuclei.


The ScaleBio scATAC Pre-Indexing Kit and analysis software enable the indexing of up to 24 samples and up to 300,000 nuclei in a single experiment. Our scATAC solution has been demonstrated on a broad range of samples types and applications.



We are developing methylation, protein, and multi-omic profiling applications to enable the discovery of biology at scale. In parallel, we are working to demonstrate our existing scRNAseq and scATACseq products in key application areas. Stay tuned for more updates on these exciting new planned products, or reach out to us if you are interested in collaborating or participating in our early access programs.

Want to learn more about or purchase our products or discuss collaboration opportunities?

Explore our available opportunities

Join us in unlocking the potential for single-cell analysis at scale and discover biology.

Companies don't do great science, people do. ScaleBio has patented disruptive technologies, a strong founding team of inventors, and a talented multidisciplinary team with a shared mission to enable researchers to unlock the potential for biological discovery at single-cell resolution. We are building a diverse, multi-disciplinary team of scientists, engineers, technologists, and bioinformaticians that share our mission for making our technology and methods more accessible to the broader research community. Are you interested in joining us?


Publications and Resources

Recent publications citing the ScaleBio combinatorial indexing technology and products and related resources.


ScaleBio Introduces New Disruptive Single-Cell Profiling and Analysis Solutions, Sets New Standards

Business Wire (2022)


Comprehensive single-cell transcriptional profiling of a multicellular organism

SCIENCE 357, 6352 (2017)

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


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 Biosciences 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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