Single-cell resolution without physical isolation

High-throughput, single-cell NGS libraries generated within a mixed cell population.

Single-cell library prep has moved inside the cell

So many questions remain regarding the genomic origins of cellular diversity, and single-cell sequencing is poised to provide answers. However, for researchers to fully embrace this technology, single-cell workflows must become simpler, more cost-effective, and accessible.

Single-cell library preparation has evolved over time—from isolating single cells into the wells of a 96-well plate, to isolating cells within droplets—but each of these methods requires the physical isolation of single cells. Factorial’s innovative in-cell library preparation technology bypasses cell isolation, enabling single-cell library preparation within a mixed cell population.


Primary biomarker: RNA, DNA
No. of partitioned reactions: 96
No. cells profiled: 96

Challenges: Highly-manual method with lower throughput. Whole genome amplification is required.


Primary biomarker: RNA, DNA, and ATAC
No. of partitioned reactions: 100,000+
No. cells profiled: 10,000-100,000+

Challenges: Limited to counting applications, small amplicon panels, and requires specialized equipment.

Split pool

Primary biomarker: RNA, ATAC
No. of partitioned reactions: 100+
No. cells profiled: 10,000+

Challenges: Cumbersome workflows and loss of low cell count/fragile cell populations. A need for costly cell isolation equipment or multiple handling steps to achieve single-cell distribution, both resulting in lower throughput.

In-cell library preparation


No. of partitioned reactions


No. cells profiled

Primary biomarker: DNA or RNA

Single-tube workflow is simpler and requires less hands-on time. High-throughput library generation from DNA or RNA that bypasses physical cell isolation.

An innovative approach: in-cell library preparation

Factorial’s innovative technology for NGS Library preparation eliminates the need for physical cell isolation for library preparation.

Nucleic acids are prepared for sequencing in one simultaneous reaction in all cells in a mixed cell suspension. Barcodes are then introduced and amplified in cells to create a combinatorial network for single-cell deconvolution.

Cost-effective and high-throughput whole genome, RNA, and target enrichment single-cell sequencing is now available to every researcher.

Tube Cell Image

In-cell library preparation generates read coverages similar to those of traditional WGS

  • Coverage distributions were compared to WGS and ATAC-Seq control sequencing data.
  • In-cell libraries had a similar coverage distribution per base more similar to that of WGS controls than ATAC-Seq.
Read Coverages Graph

Cells to sequencer in one day

Traditional single-cell library preparation methods can be complex, labor-intensive, and take 2 days.

Workflows can require:

  • Extraction and purification.
  • Multiple sample transfers between tubes and plates.
  • Multiple barcoding steps.
  • Transfer of samples into PCR tubes.
  • Separate sequencing adapter ligation.
  • Library clean up.
Factorial’s in-cell library preparation technology gives you the content flexibility of plate-based methods but with the benefit of high-throughput sample preparation.

In-cell library preparation workflow

Factorial’s technology enables the preparation of sequencing-ready libraries in one day and one tube from a mixed cell suspension.

Our streamlined single-tube workflow includes:

  • Simple buffer exchanges
  • Barcode* addition
  • In-cell amplification
  • Cell lysis and library clean up

*Barcodes are also compatible with any existing library preparation methods to support data clustering and analysis.

Let’s realize the potential of single-cell genomics.
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