Multiple human colorectal cancer datasets generated by different technologies

The human colorectal cancer datasets profiled by Visium, Visium HD, Xenium, and scFFPE-seq [ORC+25] are all available at the project website (https://www.10xgenomics.com/platforms/visium/product-family/dataset-human-crc) and the GEO DataSets database with accession number GSE280318.

• Applying RCTD and MCube to the 10x Visium CRC dataset
  • Cell type deconvolution using RCTD
  • Cell-type-specific SVG identification using MCube
• Applying RCTD and MCube to the 10x Visium HD CRC dataset
  • Cell type deconvolution using RCTD
  • Cell-type-specific SVG identification using MCube
• Applying RCTD and MCube to the 10x Xenium CRC dataset
  • Cell type deconvolution using RCTD
  • Cell-type-specific SVG identification using MCube
• Comparison of MCube results across multiple CRC datasets focusing on CAF and Macrophage
  • 10x Visium
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
  • 10x Visium HD
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
  • 10x Xenium
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
• Comparison of MCube results across multiple CRC datasets focusing on T cells
  • 10x Visium
    • Cell type deconvolution using RCTD
  • 10x Visium HD
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
  • 10x Xenium
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
• Consistency comparison of MCube, CELINA, and C-SIDE on the CRC datasets from different technologies
  • Load in scRNA-seq reference data
  • 10x Visium
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
    • Cell-type-specific SVG identification using C-SIDE
    • Cell-type-specific SVG identification using CELINA
  • 10x Visium HD
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube with different sample sizes
  • Visualization of the comparison results
    • Comparison beween MCube and CELINA
    • Comparison beween MCube and C-SIDE

References

[ORC+25]

Michelli Faria de Oliveira, Juan Pablo Romero, Meii Chung, Stephen R Williams, Andrew D Gottscho, Anushka Gupta, Susan E Pilipauskas, Seayar Mohabbat, Nandhini Raman, David J Sukovich, and others. High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer. Nature Genetics, 2025.