Spatial Transcriptomics

Achieve TRUE Single-Cell Resolution with Stereo-Seq and DNBSEQ technology

  • Unmatched Single-cell resolution 0.22 ​µm
  • Center-to-center distance 0.5 µm

What is Spatial Transcriptomics?

Spatial transcriptomics reveals cell localization and gene expression in intact tissue samples

While single-cell RNA-Seq (scRNA-Seq) can provide the novel insights of cell tissue, it has its own limitations. First, it requires to release viable cells from whole tissue without any damages or stress, making it harder to recover certain cell types, e.g. neurons in the brain. Additionally, spatial information, such as the relationship between cells and their neighboring cells within a tissue, is missing. The latest groundbreaking technology, Spatial transcriptomics, can fill this gap by discovering localization of cell types and their associated gene expression within an intact tissue sample.  In 2021, the spatial-resolved transcriptomics was named “Method of the Year 2020” by Nature Methods. This spatial transcriptomics technology allows scientists to obtain gene expression information in a spatial dimension, furthering the understanding of diseases and accelerating drug or therapy discovery.

Why use Stereo-seq technology?

Stereo-seq is the spatial transcriptomics technology that can achieve true single-cell resolution

Stereo-seq (SpaTial Enhanced Resolution Omics-sequencing) technology provides unparalleled field-of-view and subcellular resolution, allowing for simultaneous transcriptome analysis across various tissue types at multiple levels: tissue-wide, cellular, subcellular, and molecular.

Complete Genomics is the only company, offering the complete spatial transcriptomics workflow solutions. While Stereo-seq technology captures mRNA directly within tissue using a chip-based method and reconstructs cellular spatial locations through spatial coordination barcoding (Coordinate ID, CID). Meanwhile, DNBSEQ sequencing platforms provide fast, flexible, and cost-effective sequencing workflow.


True Single-cell Resolution

Stereo-seq enables unbiased transcriptome capturing at nanoscale resolution

With unbeatable nanoscale of spot size in 0.22 µm in diameter, Stereo-seq technology offers researchers a novel tool to explore spatial biology with unprecedented true single cell resolution at 0.5 µm , enabling simultaneous transcriptome study and analysis at tissue-, cellular-, subcellular- and molecular level from fresh frozen, FFPE, fixed frozen tissues.

Stereo-seq DNB chips have spots with a diameter of 0.22 µm and a center-to-center distance of 0.5 µm which provides up to 400 spots per 100 µm2, thereby allowing whole transcriptome mapping at true single cell resolution.


Stereo-seq VS Competitors

Company ​Product name​Spot size (µm)​Center-to-center distance (µm)​Capture areaSpeciesSample Type
STOmicsStereo-seq FF transcriptomics0.22​0.5​From 5 mm x 5 mm to 132 mm x 132 mmAllFresh Frozen/Fixed Frozen​
Stereo-seq OMNI10 mm x 10 mmFFPE
10x Genomics​Visium55​100​5 mm x 5 mm or 11 mm x 11 mmMouse/Human​FFPE/Fresh forzen/Fixed Frozen
Visium HD​2​N/A6.5 mm x 6.5 mmFFPE
Curio Bioscience​Seeker​10​10​3 mm x 3 mm or 10 mm x 10 mmAll Fresh Frozen

Large Capture Area

Stereo-Seq accommodates larger tissue samples by offering a centimeter-level field of view

The standard chip size for Stereo-Seq is 1 cm x 1 cm and can be expanded up to 13 cm x 13 cm. Enlarging the capture area allows the measurement of whole mammalian embryos, human organs, or model organisms.

Demonstration of Stereo-seq chip at different sizes

Species Agnostic

Stereo-seq technology supports diverse tissue types and species, and works with Fresh/Fixed frozen and FFPE samples

Stereo-seq Transcriptomics Solution utilizes a capture method for poly-adenylated mRNA capture which supports a wide range of tissue types and species including human, animals, and plants.


Using Multiplexed Multi-Omics to Study Spatial Heterogeneity in Ovarian Cancer

Studying the spatial organization of all the cells in the niche or neighborhood of a tumor is crucial to fully understand how cancers progress. Since proximity speaks to cellular activity, the spatial positioning of cells certainly plays a role in modulating clinical outcomes. However, most platforms used to reconstruct the tumor ecosystem (TE) fail to include spatial context in the three-dimensional (3D) space of a solid tumor with single-cell resolution, and thus lack information on cell-cell or cell-extracellular matrix interactions.

Featured in the Journal Cell

Spatiotemporal Transcriptomic Atlas of Mouse Organogenesis Using DNA Nanoball-patterned Arrays

Cell. 2022; 185: P1777-1792.E21, May 12, 2022

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.”

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