Xenium human breast cancer dataset

The human breast cancer datasets profiled by 10x Xenium and scFFPE-seq [JSG+23] are both available at the GEO DataSets database with accession number GSE243280.

• Random sample of 20,000 cells from the segmentation results
• Applying SPARK to the ST datasets segmented by different methods
  • Cells segmented by the 10x method
  • Cells segmented by UCS
  • Comparsion of the cell-type-specific SVG identification results
• Applying RCTD and MCube to the ST datasets segmented by different methods
  • Cells segmented by the 10x method
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
    • Negative control
  • Cells segmented by UCS
    • Cell type deconvolution using RCTD
    • Cell-type-specific SVG identification using MCube
    • Negative control
  • Comparsion of the cell-type-specific SVG identification results
  • Visualization of the identified cell-type-specific SVGs
    • Cell type DCIS 1
    • Cell type DCIS 2
• Spatial clustering of cell niches using CellCharter
• Niche-differential expression analysis using nicheDE
  • Applying RCTD and nicheDE to the ST dataset segmented by UCS
  • Comparing niche-associated genes with cell-type-specific SVGs

References

[JSG+23]

Amanda Janesick, Robert Shelansky, Andrew D Gottscho, Florian Wagner, Stephen R Williams, Morgane Rouault, Ghezal Beliakoff, Carolyn A Morrison, Michelli F Oliveira, Jordan T Sicherman, and others. High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis. Nature Communications, 14(1):8353, 2023.