Visium adult mouse brain datasets containing two biological replicates

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

• Cell type deconvolution using MacSGP
  • Visium Slice 1
  • Visium Slice 2
• Applying MacSGP to detect cell-type-specific SGPs
  • Visium Slice 1
  • Visium Slice 2
• Mouse brain dataset analysis
  • Benchmarking on Ext_Thal_1
  • MMM ct-svg results
  • Replicability analysis
• Cross sample robustness analysis on the mouse brain datasets
• Analysis of L2-regularization on the mouse brain dataset
• Robustness analysis with resampling in the mouse brain dataset
• Spatial permutation test on the mouse brain dataset
• Mouse brain (Visium): per-cell-type K selection (reproduce)
  • Part 1 — compute: synchronized per-cell-type K selection
  • Part 2 — compute: pathway enrichment of the selected SGPs (poles separated)
  • Part 3 — figures
    • 1. Cumulative held-out ΔLL vs K
    • 2. Spatial distribution of all selected SGP factors
    • 3. Pathway enrichment of the SGPs
• Results of k=10 on the mouse brain dataset

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.

[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.