Spatial Transcriptome in TME

Relying on the tumor microenvironment center technology platform, Alfa Cytology provides spatial transcriptome sequencing and analysis services for TME research, helping researchers successfully achieve their research goals.


Spatial transcriptome combines the advantages of morphological observation of histology and the advantages of high-throughput sequencing of transcriptomics to complete high-throughput sequencing of multiple sites in a tissue section. It can analyze the gene expression patterns of single cells in the tumor microenvironment (TME) in temporal and spatial dimensions, as well as the spatial location relationship and biological characteristics of cell groups, filling the gap in the research on the relationship between location and function at the tissue/organ level. It has promising application prospects in the fields of cancer, immunity, tumor-immune interaction, tumor microenvironment (TME) and tumor biology.

Overall Flow Chart of Experimental Design of Spatial Transcriptome in TMEFigure 1 Overall flow chart of experimental design (Ji A L, et al., 2020)


At Alfa Cytology, we have established a mature tumor microenvironment center technology platform, with a group of experienced tumor microenvironment research experts and mature technologies. We provide efficient spatial transcriptome sequencing and analysis services of tumor microenvironment (TME). This technology uses high-throughput sequencing data and tissue in situ barcode markers to construct a spatial expression map, explain the heterogeneity of the tumor microenvironment, and achieve a comprehensive analysis of tumor characteristics from gene expression to microenvironment. It provides a new solution for the study of microenvironment, intercellular signaling pathways and spatial heterogeneity.

Service content

Spatial Transcriptome in TME -Alfa Cytology

Standard information analysis

  • Sequencing data statistics and evaluation
  • Gene expression quantification
  • spot cluster analysis and data visualization
  • Subpopulation trait gene analysis and data visualization
  • Spatial feature gene analysis and data visualization

Advanced information analysis

  • Pseudo-time analysis
  • Association analysis with the single-cell transcriptome

Customized analysis

  • Customized information analysis can be negotiated based on customer needs.

Note: Our services list and analysis content are constantly being updated and improved, please contact us by email for more up-to-date and relevant information.

Service process

Service process

Application in tumor and microenvironment research

  • Construction of tissue in situ expression map
  • Analysis of tumor spatial heterogeneity
  • Tumor process / cell differentiation-regulation map drawing / cell developmental route fitting, etc.
  • The relationship between cell location and function in pathogenesis / regulatory network / transcription factor research

Alfa Cytology is dedicated to supporting scientists in making groundbreaking scientific discoveries and developing new applications to accelerate new drug discovery and scientific diagnosis and treatment. We have established the tumor microenvironment center technology platform with high performance scientific instruments and high value solutions to ensure high quality services that enable scientists to explore the mysteries of life at the tumor microenvironment level. Please let us know your project requirements and we will provide you with a comprehensive service from solution to report. If you have any questions, please feel free to contact us.


  1. Ji A L, Rubin A J, Thrane K, et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma[J]. Cell, 2020.

All of our services and products are intended for preclinical research use only and cannot be used to diagnose, treat or manage patients.


Alfa Cytology is a service provider specializing in tumor microenvironment research.

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