Multiple adult mouse brain datasets from different sources

The adult mouse brain dataset profiled by 10x Visium [YFL+24] is available at the project website (https://genographix.com/). The adult mouse brain dataset profiled by Spatial Transcriptomics [ONJ+20] is available at the GEO DataSets database with accession number GSE147747. The adult mouse brain snRNA-seq dataset [KSD+22] is available at the ArrayExpress with accession number E-MTAB-11115.

• Formatting the Visium data
• Cell type deconvolution using STitch3D
  • Visium Slice 1
  • Visium Slice 2
  • Integrating multiple slices profiled by Spatial Transcriptomics
• Applying MCube to multiple adult mouse brain datasets from different sources
  • Two slices of the Visium dataset
    • Visium Slice 1
    • Visium Slice 2
    • Comparing the results of the two slices
  • 3D adult mouse brain model constructed from Spatial Transcriptomics dataset
    • Visualization
• 3D visualization in the Allen Mouse Brain Common Coordinate Framework
• Applying MCube to the rotated dataset
  • Visium Slice 1
  • Visium Slice 2
  • Comparing the results before and after rotation
• Sentivity and replicability analysis of MCube
  • Visium Slice 1
    • Integrating with RCTD
    • Integrating with STitch3D
    • Comparison of the deconvolution results
    • Comparison of the cell-type-specific SVG results
    • Detailed comparison of Oligo_2
  • Visium Slice 2
    • Integrating with RCTD
    • Integrating with STitch3D
    • Comparison of the deconvolution results
    • Comparison of the cell-type-specific SVG results
  • Replicability analysis of MCube using the two slices
    • Comparison of the deconvolution results from RCTD on the two slices
    • Comparison of the cell-type-specific SVG results on the two slices

References

[KSD+22]

Vitalii Kleshchevnikov, Artem Shmatko, Emma Dann, Alexander Aivazidis, Hamish W King, Tong Li, Rasa Elmentaite, Artem Lomakin, Veronika Kedlian, Adam Gayoso, and others. Cell2location maps fine-grained cell types in spatial transcriptomics. Nature Biotechnology, 40(5):661–671, 2022.

[ONJ+20]

Cantin Ortiz, Jose Fernandez Navarro, Aleksandra Jurek, Antje Märtin, Joakim Lundeberg, and Konstantinos Meletis. Molecular atlas of the adult mouse brain. Science Advances, 6(26):eabb3446, 2020.

[YFL+24]

Yue You, Yuting Fu, Lanxiang Li, Zhongmin Zhang, Shikai Jia, Shihong Lu, Wenle Ren, Yifang Liu, Yang Xu, Xiaojing Liu, and others. Systematic comparison of sequencing-based spatial transcriptomic methods. Nature Methods, 21(9):1743–1754, 2024.