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

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.