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

ScaleBio’s 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 a compartment, enabling an accessible, instrument free, easy to adopt 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 profiled can be scaled up exponentially with repeated rounds of pooling and splitting to enable single-cell experiments with up to 96 samples and 100,00 to millions of cells, 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 up to 96 samples per experiment, with 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.

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 scATACseq chromatin accessibility library preparation pre-indexing kit and analysis software enables the indexing up to 24 samples and profiling of up to 300,000 total nuclei in a single experiment, and enables the generation of high quality profiling data at lower overall costs per sample and cell.



ScaleBio's scRNAseq 3' gene expression library preparation kit and analysis software enables the indexing of up to 96 samples and hundreds of thousands of cells in a single experiment, and enables the generation of high quality gene expression profiling to support larger and more complex studies.


ScaleBio is developing single-cell Methylation profiling, high-parameter Protein profiling, and Multi-omic solutions to broader our single-cell solutions offering. We are actively collaborating with early access tech dev partners and customers in the development of these applications. Please inquire if you are interesting in learning more about these planned solutions for 2023.

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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

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


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