This page summarizes the coverage of different brain cell types in major single-cell atlasing projects, identifying gaps in our knowledge and priorities for future characterization. Understanding atlas coverage helps interpret existing data and plan new studies.
Cell atlases vary in their coverage of brain regions, cell types, disease states, and species. This heterogeneity affects how comprehensively we can understand neurodegeneration.
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| Category | Coverage | Status |
|----------|----------|--------|
| Brain regions | 0, 75+ | Complete |
| Cell types | ~100 neuronal + glial | Complete |
| Species | Mouse | Complete |
| Human | In progress | SEA-AD |
| Single-nucleus RNA | Yes | Complete |
| Category |
Coverage |
Status |
| Brain regions |
5 cortical + hippocampus |
Complete |
| Cell types |
~80+ |
Complete |
| Subjects |
84 (AD + controls) |
Complete |
| Single-nucleus RNA |
Yes |
Complete |
| Spatial transcriptomics |
Select regions |
Complete |
| Category |
Coverage |
Status |
| Brain regions |
Multiple |
Complete |
| Cell types |
~100+ |
Complete |
| Species |
Mouse, human, marmoset |
Complete |
| Multimodal |
RNA + ATAC + protein |
Complete |
| Category |
Coverage |
Status |
| Brain regions |
100+ |
In progress |
| Cell types |
500+ |
In progress |
| Species |
Mouse, human, NHP |
Active |
| Developmental |
Full lifespan |
In progress |
| Disease focus |
AD, PD, ALS |
Active |
| Cell Type |
Atlases |
Coverage Quality |
| Glutamatergic neurons |
All |
Excellent |
| GABAergic neurons |
All |
Excellent |
| Astrocytes |
Most |
Good |
| Microglia |
Most |
Good |
| Oligodendrocytes |
Most |
Good |
| Cell Type |
Atlases |
Coverage Quality |
| OPCs |
Some |
Moderate |
| Vascular cells |
Few |
Limited |
| Meningeal cells |
Few |
Limited |
| Pericytes |
Few |
Limited |
| Cell Type |
Atlases |
Coverage Quality |
| Tanycytes |
None |
Poor |
| Radial glia (adult) |
None |
Poor |
| Ependymal cells |
Few |
Poor |
| Lymphatic cells |
None |
Poor |
| Region |
Atlases |
Notes |
| Primary motor cortex |
SEA-AD, BICCN |
Excellent |
| Prefrontal cortex |
SEA-AD, BICCN |
Excellent |
| Hippocampus |
SEA-AD |
Excellent |
| Visual cortex |
BICCN |
Excellent |
| Region |
Atlases |
Notes |
| Entorhinal cortex |
SEA-AD |
Good |
| Temporal cortex |
SEA-AD |
Good |
| Parietal cortex |
Some |
Moderate |
| Amygdala |
Few |
Limited |
| Region |
Atlases |
Notes |
| Brainstem |
Very few |
Poor |
| Hypothalamus |
Very few |
Poor |
| Thalamus |
Very few |
Poor |
| Cerebellum |
Few |
Limited |
| Spinal cord |
Few |
Limited |
| Resource |
Samples |
Coverage |
| SEA-AD |
84 |
Excellent |
| AMP-AD |
Multiple |
Good |
| Mount Sinai Brain Bank |
Multiple |
Good |
| Resource |
Samples |
Coverage |
| PD Cell Atlas |
In progress |
Limited |
| NIH Parkinson's Bank |
Multiple |
Moderate |
| Single-cell studies |
~5 |
Limited |
| Resource |
Samples |
Coverage |
| ALS Cell Atlas |
In progress |
Limited |
| Target ALS |
Multiple |
Moderate |
| Answer ALS |
Multiple |
Good |
| Atlas |
Coverage |
Quality |
| Allen Mouse Brain Cell Atlas |
Comprehensive |
Excellent |
| Tabula Muris |
Broad |
Good |
| BICCN |
Comprehensive |
Excellent |
| Atlas |
Coverage |
Quality |
| SEA-AD |
Cortex + hippocampus |
Good |
| Human Cell Atlas |
Broad |
Moderate |
| BrainSpan |
Developmental |
Good |
| Atlas |
Coverage |
Quality |
| BICCN (marmoset) |
Limited |
Moderate |
| Primate Brain Atlas |
Limited |
Moderate |
¶ Gaps and Priorities
- Brainstem cell types: Critical for PD but poorly covered
- Disease-specific atlases: Need more PD, ALS, FTD atlases
- Spatial resolution: Need more spatially-resolved transcriptomics
- Longitudinal samples: Need time-course studies
- Non-neuronal cells: Vascular, meningeal, lymphatic
- Subcortical structures: Thalamus, hypothalamus
- Aging time course: Cross-sectional vs. longitudinal
- Multi-omics integration: Transcriptomics + proteomics + epigenomics
- Cellular trajectories: Development and disease progression
- Circuit integration: Single-cell + connectomics