ARIA Xenium Spatial Transcriptomics Analysis
Project
Differential brain effects of anti-Aβ antibody treatment on Amyloid-Related Imaging Abnormalities (ARIA) in a mouse model expressing human APOE4.
Platform: 10x Genomics Xenium In Situ (480-gene targeted panel)
Samples: 6 mouse brains (C57BL/6J with human APOE4 targeted replacement) across 2 slides
| Slide | Sample | Treatment |
|---|---|---|
| Slide 1 (0021991) | KK4_465 | IgG |
| Slide 1 (0021991) | KK4_492 | Adu |
| Slide 1 (0021991) | KK4_504 | IgG |
| Slide 2 (0021998) | KK4_496 | IgG |
| Slide 2 (0021998) | KK4_502 | Adu |
| Slide 2 (0021998) | KK4_464 | Adu |
Reports
Cell type characterisation
- Cell type overview — UMAP, spatial maps, cell type proportions
- Microglia proportions — Subcluster composition by sample and brain region
Differential expression (Adu vs IgG)
- All cell types — summary — Cross-cell-type DEG overview
- All cell types — Pseudobulk DESeq2 across all cell types per brain region
- Microglia — Per brain region
- Astrocytes — Per brain region
- Endothelial — Per brain region
- Oligodendrocytes — Per brain region
- OPC — Per brain region
- Border-associated macrophages — Per brain region
- T cells — Per brain region
- Choroid plexus — Per brain region
- Ependymal — Per brain region
- Fibroblast — Per brain region
- Pericyte — Per brain region
- VLMC — Per brain region
- VSMC — Per brain region
- GABAergic neuron 1 — Per brain region
- GABAergic neuron 2 — Per brain region
- GABAergic neuron 3 — Per brain region
- GABAergic neuron 4 — Per brain region
- Glutamatergic neuron 1 — Per brain region
- Glutamatergic neuron 2 — Per brain region
- Glutamatergic neuron 3 — Per brain region
- Glutamatergic neuron 4 — Per brain region
- Glutamatergic neuron 5 — Per brain region
Astrocyte reclustering
- Astrocyte subpopulations — Reclustering at resolution 0.3, cluster identity assessment, treatment DE
- Cluster characterization — Canonical markers, proportions, pairwise DE between clusters 0, 1, and 7
- Cleaned reclustering — Removal of non-astrocyte contaminating clusters and marker genes; SCTransform and log-normalisation alternatives
- Astrocyte subcluster proportions — Propeller test for subcluster composition differences by treatment and brain region
Pathway analysis
- Microglia GSEA — Gene set enrichment by brain region (MSigDB M7 Immunologic Signatures)