STOmics Solutions

STOmics Solutions encompasses kits, software, and hardware, providing a powerful, robust, user-friendly end-to-end spatial omics product solution. It enables enables a “tissue-to-data” experience through in situ capturing of the whole transcriptome at nanoscale resolution and centimeter-sized field of view.

STOmics Solutions

Application Highlights

Detection scope

Capturing method

Sample type

Staining method

Chip size

Compatible Species

Recommended Sequencing Amount

Analysis software version

Stereo-seq Transcriptomics Solution

Unbiased spatial single-cell transcriptomics analysis, integration of tissue morphological data with high-resolution spatial transcriptome profiling, and simultaneous detection of RNA with multiplex IF(mIF) proteins.

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RNA

Poly-A

Fresh Frozen (FF)

ssDNA or H&E or immunofluorescence staining (mIF)

0.5cm * 0.5cm, 1cm * 1cm

Species agnostic

0.5cm * 0.5cm: 300~600M reads 1cm * 1cm: 1.5~2B reads

SAW v8.2 and StereoMap v4.2

Stereo-seq OMNI Solution

Enables true single-cell level spatial gene expression profiling on FFPE samples for various applications, including host-microorganism RNA co-detection.

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RNA

Random Probe

Formalin-fixed Paraffin-embedded (FFPE)

ssDNA or H&E

1cm * 1cm

Species agnostic

3B reads

SAW v8.2 and StereoMap v4.2

Stereo-seq Large Chip Designs

Unbiased spatial single-cell transcriptomics analysis for large sized tissue samples.

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RNA

Poly-A

Fresh Frozen (FF)

ssDNA or H&E

1cm * 2cm, 2cm * 2cm, 2cm * 3cm. Other large-size chips can be customized (up to 13cm * 13cm).

Species agnostic

Based on Capture Area

SAW v8.2 and StereoMap v4.2

Stereo-CITE Solution

Simultaneous profiling of unbiased whole transcriptome and high-plex proteins (100+).

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RNA

Poly-A

Fresh Frozen (FF)

DAPI

1cm * 1cm

Human and mouse

Transcriptomics: 1.5~2B reads Protein: 0.3~1B reads

SAW v8.2 and StereoMap v4.2

Analysis Software

STOmics offer comprehensive software solutions to unlock research insights.

Stereo-seq Analysis Workflow (SAW)

StereoMap is a high-definition visual desktop software to view the results of Stereo-seq data analysis. The software is designed to visualize STOmics' SpatioTemporal omics technologies and products and allows further exploration of SpatioTemporal omics data through a variety of tools provided within the software. The GEF matrix, image RPI and IPR data, and clustering results output from the SAW process can all be displayed in StereoMap.

Explore SAW Operational Manual

StereoMap

StereoMap is a high-definition visual desktop software to view the results of Stereo-seq data analysis. The software is designed to visualize STOmics' SpatioTemporal omics technologies and products and allows further exploration of SpatioTemporal omics data through a variety of tools provided within the software. The GEF matrix, image RPI and IPR data, and clustering results output from the SAW process can all be displayed in StereoMap.

Explore StereoMap Operational Manual

STOmics Instruments

STOmics offer comprehensive software solutions to unlock research insights.

Go Optical

Go Optical is a STOmics microscope manufactured by MGI, specifically designed to meet the imaging needs of Stereo-seq workflows. It employs multiple illumination techniques to capture high-resolution images with minimal stitching errors, making it ideal for tissue segmentation in Stereo-seq applications.

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Workflow

Sample Preparation

Stain and image

mRNA Capture & cDNA Synthesis

Library preparation

Sequencing

Data Analysis & Visualization

Sample Preparation

Embed, section, and mount fresh frozen or FFPE tissue sections on the Stereo-seq Chips (1cm x 2cm, 2cm x 2cm and 2cm x 3cm) or Stereo-Chip Slide (0.5cm x 0.5cm and 1cm x 1cm).

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Stain and image

Carry out tissue fixation and stain the tissue using ssDNA dye (nuclei staining, fluorescence), DAPI dye (nuclei staining, fluorescence), or hematoxylin and eosin (H&E staining, bright field) to visualize the tissue under epi-fluorescence microscopes. An upright microscope is recommended for optimal image generation.

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mRNA Capture & cDNA Synthesis

To extract mRNA from fresh frozen tissue, the tissue undergoes permeabilization, enables mRNA to bind to DNB-patterned array chips (Stereo-seq Chip T) that are preloaded with spatially-barcoded probes designed to capture and prime poly-adenylated mRNA from the tissue. To extract total RNA from FFPE tissues, the tissue is permeabilized to release RNA from cells, allowing it to bind with random probes and generate cDNA in situ (Stereo-seq Chip N). Each cDNA synthesized at a specific spot (500nm resolution) is attached to its spatially barcoded probe, enabling the subsequent spatial gene expression mapping.

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Library preparation

Stereo-seq cDNA products are used to construct a whole-transcriptome library through amplification and purification.

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Sequencing

Stereo-seq libraries can be sequenced on either DNBSEQ-T7RS or DNBSEQ-G400RS platforms using PE75 Stereo-seq Visualization Reagent set.

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Data Analysis & Visualization

Run your sequencing data on the Stereo-seq Analysis Workflow (SAW), which involves Linux command line-based pipelines, to map the sequenced reads back to their spatial locations on the tissue section, and then interactively display the results on StereoMap visualization software, a Windows/MacOS compatible desktop application.

Applications

Stereo-seq Empowers Translational Research and Drug Development

We present benchmark results comparing eight cell segmentation tools across four typical staining conditions (DAPI, ssDNA, H&E, and mIF). Our data-driven recommendations provide researchers with guidance for selecting optimal segmentation algorithms based on specific experimental conditions.

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Unveiling Tryptophan Metabolism’s Role in Tertiary Lymphoid Structures of Liver Cancer: Insights from Spatial Transcriptomics

This data-driven study not only reveals novel therapeutic targets for anti-tumor immunity, but also provides a translatable framework to dissect immune regulation in tumor microenvironments across cancers.

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Integrating Single-Cell and Spatial Transcriptomics to Decipher TME Heterogeneity in Primary vs. Metastatic Colorectal NETs

A recent study published in Molecular Cancer [1] employs single-cell technologies to investigate tumor microenvironment (TME) heterogeneity between primary tumors and liver metastases in CRNET-LM and constructs a single-cell atlas for CRNET tumor samples. The goal is to provide new insights and research avenues for enhancing the prognosis of CRNET-LM.

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Demo data

CSP Demo Data

Mouse Embryo Demo Data

Product: Stereo-seq Large Chip Designs
Kit version: Stereo-seq T FF V1.3
Species and Tissue: Mouse embryo
Embedding method: FF
Staining type: H&E staining