Single Cell Library Preparation Kits@2x


Single Cell RNA Sequencing Kit

Enables single cell RNA sequencing across dozens of samples with 125,000 cells or nuclei in parallel.


The ScaleBio Single Cell RNA Sequencing Kit enables the production of high-quality single-cell transcriptomic libraries. Our upfront cell fixation step allows you to take a flexible approach to sample collection, whether from multiple sites or multiple timepoints. This approachable 2-day workflow let's you profile up to 125,000 cells or nuclei as well as multiplex up to 96 samples in a single experiment.


Cell Atlasing

Disease Research

Large Patient Cohort Analysis

Biomarker Discovery

ScaleBio high-throughput single cell sequencing kit workflow diagram


Single cell or nuclei suspensions are prepared and fixed using the ScaleBio Sample Fixation Kit. Samples can be used immediately or stored. Cells or nuclei are then barcoded through three split-pool indexing rounds to produce a sequence-ready library. Data is analyzed with the ScaleBio RNA pipeline.

Example clustering data produced from ScaleBio single cell combinatorial indexing of PBMCs

Unravel sample heterogeneity to discover biology

Over 125,000 PBMCs were profiled to explore cellular heterogeneity within a complex sample type. The UMAP clustering data demonstrates the cell type and cell state heterogeneity of the sample, all easily identified with ScaleBio’s sensitive single cell combinatorial indexing chemistry.


Sample Compatibility

Single cell or nuclei suspensions


1 - 96 samples per run


125,000 cells or nuclei

Multiple rate


Comprehensive single cell transcriptional profiling of a multicellular organism.

Science 357, 6352 (2017)

The single-cell transcriptional landscape of mammalian organogenesis.

Nature 566, 496-502 (2019).

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

Commun Biol 3, 213 (2020).

Single Cell RNA Sequencing resources

Frequently asked questions

Together with our customers, we have demonstrated performance of our Single Cell RNA Sequencing Kit across a broad range of cell types, including but not limited to: tissue-dissociated cells, nuclei isolated from frozen and fresh tissues, PBMCs, and cell lines.

After fixation, samples can be stored immediately at -80C or transported on dry ice and then stored at -80C. Current storage times are up to 1 month. This is expected to be extended after further validation studies.

The first distribution of cells into the Reverse Transcription (RT) plate assigns a well-specific barcode that is used to identify the sample(s) during data analysis. Samples can be distributed across multiple wells for deeper sample profiling, or each well can contain an individual sample for maximum sample throughput.

ScaleBio provides a downstream data analysis pipeline, which is compatible with sequencing instrument output files. The pipeline will de-multiplex samples, generate a cell-gene matrix, as well as provide a data quality metrics summary to assess run performance.

ScaleBio RNA libraries have been demonstrated with MiSeq, NextSeq and NovaSeq instruments.


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Single Cell Library Preparation Kits@2x

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