hippo-seq

Hippocampus Cell Atlas

  • A harmonised single-cell transcriptomic atlas of the mouse hippocampus
  • Early post-hypoxia and ischemia transcriptomic atlases.

Article Link (to be filled)

* The image is adapted from Slide-seq v2 dataset of mouse hippocampus by integrating it with our HCA atlas.

Datasets & Data analysis

Hippocampus Cell Atlas (HCA)

Integrated mouse scRNA-seq atlas (>400k cells)


  • Interactively explore hippocampus cell types
  • Investigate gene expression and co-expression patterns
  • Analyze your data by overlaying user-provided gene sets
Go to HCA atlas

Post- hypoxia and ischemia

Early changes post- hypoxia and ischemia snRNA-seq atlas (>24k cells)


  • Atlas includes 3 datasets: Healthy Control (HC), Post-Hypoxia, and Post-Hypoxia with Ischemia.
  • Investigate gene expression and co-expression patterns, and overlay your gene sets onto both pathological and healthy conditions.
Go to H&I atlas

Data analysis

sc/nRNA-seq analysis of user provided data

  • Discover what cell types your transcriptomics and spatial data correspond to. Extract cluster-specific differentially expressed genes from your data and overlay on the atlases to see corresponding cell types.

  • Overlay disease-associated genes to identify potential involvement in specific hippocampal cell types or pathological conditions.

  • Automatically assign cell types for Hippocampus through R or Python with ScType using our ML-based identified hippocampus markers.