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Spatial Transcriptomics
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What is Spatial Transcriptomics?
Spatial transcriptomics is an innovative technology that enables scientists to map gene expression within the structural context of tissues.
This approach not only identifies which genes are active but also reveals their precise locations within the tissue. By providing spatially resolved data, it offers deeper insights into cellular interactions and tissue organization, which are crucial for studying tissue heterogeneity, disease progression, and developmental processes. Unlike conventional transcriptomics, which analyzes gene expression in bulk, spatial transcriptomics delivers a detailed “Google map” of where genes are expressed within a tissue sample.
This technology has significant applications across multiple fields. In cancer research, it helps scientists examine how tumor cells interact with their surrounding microenvironment, paving the way for disease mechanism research, more targeted therapies, etc. In neuroscience, spatial transcriptomics allows researchers to map neural circuits and understand how gene expression influences brain function. By answering complex questions about tissue function, cellular environments, and disease mechanisms, spatial transcriptomics accelerates advancements in precision medicine and the development of new treatments. It was recognized as the "Method of the Year 2020" by Nature Methods, highlighting its growing importance in biological research.
Why Stereo-seq
Technology introduction
STOmics' proprietary Stereo-seq (SpaTial Enhanced REsolution Omics-sequencing) technology provides researchers with a revolutionary sequencing-based tool for spatial biology discovery. Stereo-seq is capable of obtaining whole transcriptome information without pre-designed probes at true single-cell resolution and centimeter-level field-of-view. Stereo-seq has proven performance on multiple tissue samples across different species. This advanced spatial-omics platform is compatible with fresh frozen and formalin-fixed-paraffin-embedded (FFPE) tissue samples. Over 100+ papers have been published in top journals, such as Science, Nature, and Cell, during the past two years.
How Stereo-seq works
Stereo-seq Technology Highlights
True Single-Cell Resolution
The silicon-based Stereo-seq chip features densely patterned RNA-capturing spots, each labeled with a unique spatial coordinate barcode (Coordinate ID, CID). With a center-to-center distance of just 0.5 µm between adjacent spots, it enables transcriptome studies and analysis at true single-cell resolution. Each cell, approximately 10 µm in diameter, is captured by 400 spots. A standard-sized Stereo-seq chip (1 cm x 1 cm) contains 400 million RNA-capturing spots.
Large Capture Area for Comprehensive Analysis
Demonstration of Stereo-seq chip at different sizes
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.
Species Agnostic
Stereo-seq technology supports diverse tissue types and species, and works with Fresh 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.
Wide range of Human tissue types
Brain
Thymus
Lymph
Liver
Ovary
Small Intestine
Kidney
Prostate
Endometrium
Muscle
Epileptic Hippocampus
Tonsil
Skin hairfollicle
Brain cancer
Breast cancer
Liver cancer
Pancreatic cancer
Lung cancer
Thyroid cancer
Esophageal cancer
Kidney cancer
Colon cancer
Endometrial carcinoma
Lymphnode metastasis
Wide range of Mouse tissue types
Head
Whole brain
Eye ball
Tongue
Heart
Skin
Spleen
Large intestine
Small intestine
Lung
Kidney
Liver
Thymus
Bulbus oculi
Ovary
Olfactory bulb
Pancreas
Colon
Cecum
Testis
Spinal cord
Placenta
More Species tissue types
Arabidopsis
Soy bean
Drosophila
Zebra fish
Salamander
Macaque
STOmics products
Stereo-seq Transcriptomics
STOmics Stereo-seq v1.3 captures whole transcriptomes in situ at nanoscale resolution across centimeters. New chemistry, probes, and enzymes deliver improved efficiency and streamlined workflow.
Stereo-seq Transcriptomics H&E
Stereo-seq Transcriptomics H&E integrates tissue phenotyping and spatial molecular profiling. Using H&E-stained morphology, it aids tissue identification, ROI profiling, and differential analysis.
Stereo-seq Large Chip Designs
STOmics Stereo-seq Transcriptomics LCD enables in situ whole-transcriptome capture of entire tissue sections at nanoscale resolution on large chips (up to 2×3 cm), compatible with all species.
Stereo-seq Transcriptomics mIF
Stereo-seq mIF combines whole transcriptomics, protein detection, and tissue morphology on the same tissue slice, enabling spatial multi-omics at single-cell resolution without affecting mRNA capture.
Stereo-CITE
Stereo-CITE uses CITE-seq to detect whole transcriptomes and 100+ proteins on the same tissue section, facilitating study of tissue heterogeneity in complex diseases and broadening spatial omics understanding.
Stereo-seq OMNI
Stereo-seq OMNI offers spatial single-cell total RNA analysis of FFPE samples using 'Random Probe' design, covering 10×10 mm areas with precise transcriptomics.
Check Our Demo Results
Exploring true spatial single-cell total RNA information with Stereo-seq OMNI by clicking any of the cards below.
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Frequently Asked Questions
Highlighted in the Cell Journal
Spatiotemporal Transcriptomic Atlas of Mouse Organogenesis Using DNA Nanoball-patterned Arrays
