Our Technology

How combinatorial indexing enables scalable single cell sequencing

Our single cell technology platform uses combinatorial barcoding of analytes within cells themselves (cDNA, DNA, Protein) which eliminates the requirement for specialized cell partitioning instrumentation.

Cells or nuclei are passed through a series of barcoded wells using our patented split and pool methodology, uniquely labeling cells and their analytes (e.g. cDNA). This exponentially scalable technology enables barcoding of millions of cells with only several barcoded multi-well plates. Using next-generation sequencing, each single cell profile is deconvoluted and it's analyte profile assembled.

The technology is scalable, profiling 100’s of samples and 100,000 to millions of cells per experiment. Flexible, fixation enables storage and batching of samples. This instrument-free workflow only requires reagent kits, basic laboratory equipment, and simple plastics. Our technology and methods are both compatible with and independent of on-market single cell systems.


Our combinatorial indexing technology for single cell sequencing enables unprecedented sample indexing and cell throughput across a broad range of genomic, proteomic, and multi-omic applications to enable researchers to discover biology at scale.

Scalable sample indexing
Scalable sample multiplexing

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.

Watch how combinatorial indexing has 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 library preparation kits

Single Cell RNA Kit

Enables single-cell gene expression profiling for up to 96 samples and 125,000 cells per experiment.

Single Cell ATAC Kit

Enables the analysis of open chromatin accessibility at the single-cell level for profiling cell states and for understanding gene regulatory mechanisms.

Founders behind the technology

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.

-g-Scientific founders Image@2x
Comprehensive single-cell transcriptional profiling of a multicellular organism

Science 357, 6352 (2017).

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

Commun Biol 3, 213 (2020).

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

Nature Communications (2022)