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Spatially Map Gene Expression at Single-Cell Level in The Tissue Context to Promote the Research of SARS-CoV-2.

Spatial single-cell sequencing (mainly single-cell RNA-seq, scRNA-seq) combines single-cell technology and spatially resolved transcriptomics to systematically map the molecular and cellular composition during infection. It provides new ways to explore viral diversity and cell response to viral infection, including the widely-spreading SARS-CoV-2 (COVID-19). As one of the most reliable suppliers for single-cell sequencing and analyses, Creative Biolabs provides high-throughput single cell spatial gene expression profiling services to create new multidimensional modalities associated with COVID-19 therapeutics.

What Is Single-cell Spatial Mapping of Gene Expression?

Single-cell spatial gene expression mapping requires the integration of 1) spatial information with 2) RNA-seq profiling at a single-cell level.

1) The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during virus infection. It can also help us understand the complex crosstalk and communication between neighboring cell-types, providing invaluable insights into infection-relevant molecular mechanisms and processes.

2) scRNA-seq has emerged as an indispensable tool to dissect the cellular heterogeneity, leading to a comprehensive understanding of the micro-environment and dynamic infection processes. It has been widely used to study differences between host cell types and subpopulations which are associated with virus entry and transmission.

Spatial transcriptomics at single-cell level.Fig.1 Spatial transcriptomics at the single-cell level. (Maynard, 2019)

Spatially scRNA-seq allows the characterization of spatial organization of cells in tissues, which revolutionizes the studies of tissue function and disease pathology, such as COVID-19.


  • Analysis of individual cellular heterogeneity of complex organs with the spatial information;
  • Spatially map scRNA-seq gene profiles at the single-cell level in the tissue context;
  • Identification of rare cell types, potential therapeutic markers, and cellular signaling pathways;
  • Providing new insights to better understand the complex biology of infection.

Services at Single Cell

Based on our spatially scRNA-seq platform, Single Cell provides a suite of scRNA-seq sequencing and analyses to comprehensively characterize the spatial gene expression changes of different tissues/cells, so as to speculate the possible genes involved in the virus entry and conclude which cell type may be more vulnerable to SARS-CoV-2 infection. In addition, we fully integrate spatial information and the detection of differential expression to identify linear or periodic expression patterns, capture multiple dimensions of infection and the immune response (e.g. cellular phenotypes, adaptive immune repertoire and antigen specificity, spatial resolution of immune tissue infiltration), to reveal the fundamental molecular and cellular basis for complex pathophysiological signatures.

Single Cell Spatial Gene Expression for SARS-CoV-2 (COVID-19) Research

Based on the SARS-CoV-2, we have applied single-cell transcriptome analyses to study the spatial expression patterns of ACE2 in various tissues and cell types of the human body from COVID-19+ patients to clearly reveal the entry mechanism of the virus. We used scRNA-seq combined with single-molecule fluorescence in-situ hybridization (smFISH) to view global gene expression patterns in three dimensions. We found that viral transmissivity is dependent on ACE2 receptor accessibility based on spatial distribution along the respiratory tract.

Spatially scRNA-seq combined with smFISH.Fig.2 Spatially scRNA-seq combined with smFISH.


  • The original sequencing data
  • Detailed data analysis report
  • Tailored experimental results

Spatial scRNA-seq provides quantitative gene expression data and visualization of the protein distribution map with high sensitivity & specificity at single-cell resolution. It enables novel types of bioinformatics analyses, valuable in SARS-CoV-2 research, diagnostics, and treatment. Creative Biolabs is being focused on the single-cell spatial gene expression mapping to elucidate the mechanism of virus entry or transmission. If you have additional requirements or questions, please feel free to contact us.


  1. Maynard, K.R.; et al. Spatial transcriptomics: putting genome-wide expression on the map. Neuropsychopharmacology. 2019.
! ! For Research Use Only. Not for diagnostic or therapeutic purposes.