Alzmap is a data website accompanying our "Spatial transcriptomics and in situ sequencing uncover coordinated cell responses to amyloid-β plaques in Alzheimer’s disease" paper, created at the Bart de Strooper laboratory for research of neurodegenerative diseases in Leuven, Belgium.


While complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here in an AD mouse model the transcriptional changes occurring in tissue domains of 100 μm diameter around the amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIG), while a multicellular gene coexpression network of Plaque-Induced Genes (PIGs) involving the complement system, oxidative stress, lysosomes and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomic analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.

This Website

This website provides a number of methods to interactively explore the spatial transcriptomics datasets.

Interactive Figures

These links provide explorable versions of the figures in the paper. Note, there may minor changes, for example in colors used, compared to the figures in the paper.
  • Figure 1:   1C,   1C (PCA1/2),   1D,   1D (PCA1/2)
  • Figure 2:   2C
  • Figure 3:   3B,   3C,   3E and 3F
  • Figure 4:  
  • Figure 6:   6A and 6B,   6C
  • Supplemental Figure S1:   S1G,   S1H (Dsp),   S1H (Wfs1),   S1H (Prox1),   S1H (Fibcd1),   S1I (mt-Co1),   S1I (Hba-a1),   S1I (Aldoc),   S1I (Gfap)
  • Supplemental Figure S3:   S3A,   S3B
  • Supplemental Figure S5:   S5A,   S5C