Stereo-seq Technology
Achieve True Single Cell Resolution
Stereo-seq
Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing) is a sequencing-based spatial transcriptomics technology that combines nanometer-scale resolution with an ultra-large capture area, enabling researchers to visualize gene expression across tissues with unprecedented detail and scale. It leverages DNA Nanoball (DNB)-based patterned arrays with spot diameters of 0.22 μm, offering true single-cell and subcellular resolution. Species agnostic by design, Stereo-seq can be applied across a wide range of organisms – from human to plants.
Leading spatial innovation: 120+ peer reviewed articles using Stereo-seq published in top journals Science, Nature, and Cell like since 2022.
Stereo-seq + DNBSEQ Spatial Transcriptomics Workflow
Stereo-seq, combined with DNBSEQ sequencing, delivers a complete and cost-effective spatial transcriptomics solution with true single-cell resolution. The DNBSEQ-T7 platform is highly recommended for spatial transcriptomics due to its exceptional accuracy, flexibility, and cost efficiency.
Achieve true single cell resolution
Stereo-seq achieves true single-cell resolution by leveraging DNBSEQ technology on a silica-based chip. This chip features a patterned array of capture spots spaced 500 nm apart (center-to-center), each functionalized with DNA probes composed of three key components:
- Coordinate ID (CID): Uniquely identifies the spatial position
of each capture spot, enabling precise spatial mapping of
transcripts. - Molecular Identifier (MID): A random sequence used to
distinguish between original mRNA molecules and PCR
duplicates, allowing for accurate molecule counting. - Poly-T tail or randomers: Capture polyadenylated mRNA or
a broader range of RNA species, ensuring comprehensive
transcript detection.
Single-Cell Spatial Gene Expression via Custom Pipeline
A custom bioinformatics pipeline processes the data to reconstruct spatial gene expression at single-cell resolution. Spatial bins—such as “Bin 20,” which approximates a single cell—can be adjusted by researchers based on the desired resolution and specific experimental needs. Alternatively, a nuclei or H&E stained image can be used to achieve more accurate cell segmentation and single-cell level gene expression results.
Large Capture Area
Stereo-seq offers a range of chip sizes to accommodate diverse tissue and organ research needs—from formats smaller than 1 cm × 1 cm to large-scale chips up to 13 cm × 13 cm. This flexibility enables researchers to tailor experiments based on sample size, resolution, and biological context. Its scalability supports spatial transcriptomics profiling of entire mammalian embryos, human organ sections, and large model organisms.
Unlike most spatial transcriptomics platforms, which are restricted to
smaller capture areas, Stereo-seq uniquely combines true single-cell resolution with a significantly expanded field of view—making it a powerful tool for high-throughput, whole-organ analysis.
Species Agnostic
Stereo-seq supports a wide range of tissue types and species, working with fresh/fixed-frozen, and FFPE samples. By capturing polyadenylated mRNA or a broader range of RNA species, it enables spatial transcriptomics across humans, animals, and plants. This flexibility makes Stereo-seq ideal for diverse research areas—from biomedical and agricultural studies to evolutionary biology.
Stereo-seq outperforms competitors with the smallest spot size and highest resolution
| Company | Product name | Spot size (µm) | Center-to-center distance (µm) | Capture area | Species | Sample Type |
|---|---|---|---|---|---|---|
| STOmics | Stereo-seq transcriptomics | 0.22 | 0.5 | From 5 mm x 5 mm Up to 132 mm x 132 mm | All | Fresh Frozen Fixed Frozen |
| Stereo-seq OMNI | 0.22 | 0.5 | 10 mm x 10 mm | All | FFPE | |
| 10x Genomics | Visium | 55 | 100 | 5 mm x 5 mm 11 mm x 11 mm | Human Mouse | Fresh Frozen Fixed Frozen FFPE |
| Visium HD | 2 | 2 | 6.5 mm x 6.5 mm | Human Mouse | FFPE | |
| Curio Bioscience | Seeker | 10 | 10 | 3 mm x 3 mm 10 mm x 10 mm | All | Fresh Frozen |
Pathology and Spatio-Temporal Analysis in One Section
Our innovative staining method enables the integration of pathology study and spatio-temporal analysis on a single tissue section.
Large field of view and high resolution
Using the decimeter-scale STOmics Chip and nanoscale DNB probes, subcellular details can be captured from any location on an entire tissue section.
Multidimensional analysis
Enabled the integration of tissue staining studies with whole-genome mRNA transcriptomics and proteomics.
Excellent compatibility
Stereo-seq is compatible with fresh frozen samples and performs reliably on cells, organs, and embryo sections across various animal and plant species.
Applications
With widespread application in spatio-temporal atlases, species evolution, disease diagnosis, therapy, and prognosis, Stereo-seq and its future technical advancements promise to be transformative across multiple research fields.
This technology will deepen our understanding of human life and help redefine disease.
Connect with our experts
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