Visium human dorsolateral prefrontal cortex dataset

The human DLPFC dataset profiled by 10x Visium [MCTW+21] is available at the project website (https://research.libd.org/spatialLIBD/). The human DLPFC snRNA-seq dataset profiled by 10x Genomics Chromium [NMT+20] is available at the GEO DataSets database with accession number GSE144136.

• Cell type deconvolution using STitch3D
• Applying MCube to the DLPFC dataset
  • Applying MCube to each ST slice seperately
    • Visualization of the deconvolution results of the first slice
    • Visualization of the cell type-specific SVG results
  • Negative control using one slice
  • Applying MCube to the integrated four ST slices together
    • Visualization of the cell type-specific SVG results from the 3D perspective
    • Visualization of the platform effects across slices
  • Comparison of the 2D and 3D results
• Comparison with the methods not considering cell type mixtures
  • Methods not considering cell type mixtures
  • Comparison of the SVG identification results

References

[MCTW+21]

Kristen R Maynard, Leonardo Collado-Torres, Lukas M Weber, Cedric Uytingco, Brianna K Barry, Stephen R Williams, Joseph L Catallini, Matthew N Tran, Zachary Besich, Madhavi Tippani, and others. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience, 24(3):425–436, 2021.

[NMT+20]

Corina Nagy, Malosree Maitra, Arnaud Tanti, Matthew Suderman, Jean-Francois Théroux, Maria Antonietta Davoli, Kelly Perlman, Volodymyr Yerko, Yu Chang Wang, Shreejoy J Tripathy, and others. Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons. Nature Neuroscience, 23(6):771–781, 2020.