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Spatial Multi-Omics Solutions

Spatial Multi-Omics Solutions CapitalBio

CapitalBio Technology owns 3 spatial omics platforms, 10x Genomics Visium、Nanostring GeoMx Digtal Spatial Profiler and SEAM, enables spatial multi-omics detection of fresh-frozen samples and FFPE samples. At present, 500+ samples and 50+ different sample types have been completed, covering species and sample types including human and mouse brain, eyeball, oral cavity, heart, liver, lung, kidney, intestine, stomach, ovary, prostate, bladder, skin, etc.

10X Genomics Visium

Visium Spatial Transcriptome Sequencing Utilizes the 10x Genomics Visium platform, combined with microscopic imaging, targeted probe capture, chips, and sequencing technologies, to obtain transcriptome data in cells at different positions of the slice from a complete frozen tissue section or paraffin tissue section, and combine histology and gene expression analysis, and visualize gene expression and morphological data through unique data analysis methods.

Applications Advantages Example 1
  • Tumor research: Tumor microenvironment, tumor heterogeneity, tumor immunity, discovery of potential tumor biomarkers

  • Developmental biology: Spatiotemporal atlas of organogenesis

  • Neuroscience: Spatio-Temporal Atlas changes in key brain regions, neurological diseases

  • Disease and immunity: Spatial molecular pathology research, immune microenvironment.

Self-developed a variety of special tissue permeabilization methods

Leica microtome, Leica/Nikon microscope imaging system, Illumina sequencer

10x Genomics CSP official certification service provider

Spatial in situ global analysis of whole transcriptome profiles

Integrating single-cell RNA sequencing with spatial transcriptomics reveals immune landscape for interstitial cystitis [Supported by CapitalBio Technology]

Journal: Signal Transduction and Targeted Therapy   IF: 38.1027


Interstitial cystitis/bladder pain syndrome (IC/BPS) is currently the most difficult disease in the field of gynecology and urology. The main clinical manifestations are frequent urination and severe pain in the overflow bladder. The disease has existed for more than 100 years, but the etiology is still unknown, what role immunity plays in the development of IC, and at which stage of the IC process it exerts its effector effect.




1.IC Bladder Immunogram

A total of 135,091 CD45+ immune cells were captured from the bladders of IC patients and controls for identification and grouping and construction of IC immune profiles. Re-clustering analysis of T cells revealed that CD8+ T cells in the IC group had impaired efficacious function and reduced pathogen clearance ability. B cell re-clustering analysis revealed a strong humoral immune response in the IC bladder, and IgE can be used as a potential rapid diagnostic marker for IC.


Figure 1. Workflow and IC Bladder Immunogram

2.Clustering and grouping with spatial transcriptomics

The IC and control bladder were taken for spatial transcriptomics, cluster analysis and group identification, and were divided into 8 clusters in total.


Figure 2. IC and Control Bladder Spatial Transcriptome Atlas

3.MIA analysis of spatial transcriptomics and scRNA-seq reveals differential distribution of immune cells in IC versus control bladder

Gene characterization by spatial transcriptomic studies found that fibrosis-associated genes were highly expressed in different cell types in the IC group, again suggesting the possibility of severe fibrosis in the patient's bladder. Using MIA combined with single-cell data and spatial data, it was found that almost all immune subsets in IC bladder were enriched in the urothelial area or near fibroblasts, and the results again confirmed the importance of urothelial cells and fibroblasts in the pathogenesis of IC effect.

Figure 3. Differential distribution of immune subgroups in IC and control bladders after combining single-cell and spatial data

Nanostring GeoMx Digtal Spatial Profiler

Based on the GeoMx Digital Spatial Profiler developed by NanoString, the combination of histopathology, immunology and molecular techniques is used to obtain multi-omics target information in multiple specific target regions, realize the in situ detection of protein and gene information on frozen tissue or paraffin tissue sections, which can be called a biological GPS positioning system.

Applications Advantages

Tumor research: Tumor microenvironment, tumor heterogeneity, tumor immunity, the discovery of potential tumor biomarkers

Infection and immunity: Immune response to disease infection, immune microenvironment

Developmental biology: Describe the developmental formation of anatomically characteristic regions and study the complex gene regulation that drives growth and development

Neurology: neurodegenerative disease, neuroimmune

  • Quantitative analysis of RNA and protein in spatially defined regions

  • In situ quantification of human and mouse gene-wide transcript profiles or up to 100+ proteins on a single tissue section

  • Combine tissue morphology information from 1-4 fluorescent antibody staining with gene expression or protein quantification to obtain cell type-specific molecular expression information



Based on SEAM technology, the platform requires no sample labeling, no special matrix, and is highly sensitive. Through a simple sample preparation process, TOF-SIMS provides sub-micron ultra-high spatial resolution metabolic detection and specialized algorithms to describe tissue metabolism at the single-cell level in situ microenvironment.

Applications Advantages

Tumor immunology: Tumor metabolic biomarkers, tumor metabolic microenvironment, tumor immune response and escape, tumor metabolic reprogramming

Developmental biology: Metabolic regulation and metabolic mapping in organ and embryonic development

Drug discovery: Pharmacodynamic mechanism, pharmacokinetics, drug toxicology

Disease pathology: Molecular mechanism of metabolism, endogenous and exogenous metabolites in lesion center

Plant research: Plant biotic and abiotic stress, plant-environment interaction, localization of medicinal plant components


  • The only submicron spatial resolution imaging mass spectrometer

  • The only professional SEAM analysis pipeline, the latest dedicated SEAM algorithm

Papers supported by Capitalbio Technology based on the Spatial Platforms

PaperA pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcriptionIdentification of HSC/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomicsSpatial transcriptomics reveals gene expression characteristics in invasive micropapillary carcinoma of the breastA missing piece of the puzzle in pulmonary fibrosis: anoikis resistance promotes fibroblast activationIntegrating single-cell RNA sequencing with spatial transcriptomics reveals immune landscape for interstitial cystitisGREM1/PPP2R3A expression in heterogeneous fibroblasts initiates pulmonary fibrosisIntegrating microarray-based spatial transcriptomics and single-cell RNA-sequencing reveals tissue architecture in esophageal squamous cell carcinoma
JournalNature CommunicationsCell ResearchCell Death & DiseaseCell & BioscienceSignal Transduction and Targeted TherapyCell and BioscienceEBioMedicine

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