Cell Atlas Coverage

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Cell Atlas Coverage

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wiki page Created: 2026-04-02T07:19:40 By: crosslink-migration Quality: 50% ✓ SciDEX ID: wiki-cell-types-cell-atlas-coverage

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Cell Atlas Coverage

Overview

...

Cell Atlas Coverage

Overview

Mermaid diagram (expand to render)

<table class="infobox infobox-cell">
<tr>
<th class="infobox-header" colspan="2">Cell Atlas Coverage</th>
</tr>
<tr>
<td class="label">Category</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">Brain regions</td>
<td>0, 75+</td>
</tr>
<tr>
<td class="label">Cell types</td>
<td>~100 neuronal + glial</td>
</tr>
<tr>
<td class="label">Species</td>
<td>Mouse</td>
</tr>
<tr>
<td class="label">Human</td>
<td>In progress</td>
</tr>
<tr>
<td class="label">Single-nucleus RNA</td>
<td>Yes</td>
</tr>
<tr>
<td class="label">Category</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">Brain regions</td>
<td>5 cortical + hippocampus</td>
</tr>
<tr>
<td class="label">Cell types</td>
<td>~80+</td>
</tr>
<tr>
<td class="label">Subjects</td>
<td>84 (AD + controls)</td>
</tr>
<tr>
<td class="label">Single-nucleus RNA</td>
<td>Yes</td>
</tr>
<tr>
<td class="label">Spatial transcriptomics</td>
<td>Select regions</td>
</tr>
<tr>
<td class="label">Category</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">Brain regions</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Cell types</td>
<td>~100+</td>
</tr>
<tr>
<td class="label">Species</td>
<td>Mouse, human, marmoset</td>
</tr>
<tr>
<td class="label">Multimodal</td>
<td>RNA + ATAC + protein</td>
</tr>
<tr>
<td class="label">Category</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">Brain regions</td>
<td>100+</td>
</tr>
<tr>
<td class="label">Cell types</td>
<td>500+</td>
</tr>
<tr>
<td class="label">Species</td>
<td>Mouse, human, NHP</td>
</tr>
<tr>
<td class="label">Developmental</td>
<td>Full lifespan</td>
</tr>
<tr>
<td class="label">Disease focus</td>
<td>AD, PD, ALS</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">Glutamatergic neurons</td>
<td>All</td>
</tr>
<tr>
<td class="label">GABAergic neurons</td>
<td>All</td>
</tr>
<tr>
<td class="label">Astrocytes</td>
<td>Most</td>
</tr>
<tr>
<td class="label">Microglia</td>
<td>Most</td>
</tr>
<tr>
<td class="label">Oligodendrocytes</td>
<td>Most</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">OPCs</td>
<td>Some</td>
</tr>
<tr>
<td class="label">Vascular cells</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Meningeal cells</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Pericytes</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">Tanycytes</td>
<td>None</td>
</tr>
<tr>
<td class="label">Radial glia (adult)</td>
<td>None</td>
</tr>
<tr>
<td class="label">Ependymal cells</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Lymphatic cells</td>
<td>None</td>
</tr>
<tr>
<td class="label">Region</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">Primary motor cortex</td>
<td>SEA-AD, BICCN</td>
</tr>
<tr>
<td class="label">Prefrontal cortex</td>
<td>SEA-AD, BICCN</td>
</tr>
<tr>
<td class="label">Hippocampus</td>
<td>SEA-AD</td>
</tr>
<tr>
<td class="label">Visual cortex</td>
<td>BICCN</td>
</tr>
<tr>
<td class="label">Region</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">Entorhinal cortex</td>
<td>SEA-AD</td>
</tr>
<tr>
<td class="label">Temporal cortex</td>
<td>SEA-AD</td>
</tr>
<tr>
<td class="label">Parietal cortex</td>
<td>Some</td>
</tr>
<tr>
<td class="label">Amygdala</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Region</td>
<td>Atlases</td>
</tr>
<tr>
<td class="label">Brainstem</td>
<td>Very few</td>
</tr>
<tr>
<td class="label">Hypothalamus</td>
<td>Very few</td>
</tr>
<tr>
<td class="label">Thalamus</td>
<td>Very few</td>
</tr>
<tr>
<td class="label">Cerebellum</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Spinal cord</td>
<td>Few</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>Samples</td>
</tr>
<tr>
<td class="label">SEA-AD</td>
<td>84</td>
</tr>
<tr>
<td class="label">AMP-AD</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Mount Sinai Brain Bank</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>Samples</td>
</tr>
<tr>
<td class="label">PD Cell Atlas</td>
<td>In progress</td>
</tr>
<tr>
<td class="label">NIH Parkinson's Bank</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Single-cell studies</td>
<td>~5</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>Samples</td>
</tr>
<tr>
<td class="label">ALS Cell Atlas</td>
<td>In progress</td>
</tr>
<tr>
<td class="label">Target ALS</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Answer ALS</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">Atlas</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">Allen Mouse Brain Cell Atlas</td>
<td>Comprehensive</td>
</tr>
<tr>
<td class="label">Tabula Muris</td>
<td>Broad</td>
</tr>
<tr>
<td class="label">BICCN</td>
<td>Comprehensive</td>
</tr>
<tr>
<td class="label">Atlas</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">SEA-AD</td>
<td>Cortex + hippocampus</td>
</tr>
<tr>
<td class="label">Human Cell Atlas</td>
<td>Broad</td>
</tr>
<tr>
<td class="label">BrainSpan</td>
<td>Developmental</td>
</tr>
<tr>
<td class="label">Atlas</td>
<td>Coverage</td>
</tr>
<tr>
<td class="label">BICCN (marmoset)</td>
<td>Limited</td>
</tr>
<tr>
<td class="label">Primate Brain Atlas</td>
<td>Limited</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>URL</td>
</tr>
<tr>
<td class="label">Allen Brain Atlas</td>
<td>portal.brain-map.org</td>
</tr>
<tr>
<td class="label">SEA-AD</td>
<td>portal.brain-map.org</td>
</tr>
<tr>
<td class="label">BICCN</td>
<td>biccn.org</td>
</tr>
<tr>
<td class="label">BICAN</td>
<td>knowledge.brain-map.org</td>
</tr>
<tr>
<td class="label">Human Cell Atlas</td>
<td>humancellatlas.org</td>
</tr>
<tr>
<td class="label">Broad Institute</td>
<td>singlecell.broadinstitute.org</td>
</tr>
</table>

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. [@allen2023]

Cell atlases vary in their coverage of brain regions, cell types, disease states, and species. This heterogeneity affects how comprehensively we can understand neurodegeneration. [@biccn2021]

--- [@human2022]

Major Atlas Projects

Allen Brain Cell Atlas

SEA-AD (Seattle Alzheimer's Disease Brain Cell Atlas)

BICCN (Brain Initiative Cell Census Network)

BICAN (Brain Initiative Cell Atlas Network)

Coverage by Cell Type

Well-Covered Cell Types

Moderately Covered Cell Types

Under-Covered Cell Types

Regional Coverage

Well-Covered Regions

Moderately Covered Regions

Under-Covered Regions

Disease State Coverage

Alzheimer's Disease

Parkinson's Disease

ALS

Species Coverage

Mouse

Human

Non-Human Primate

Gaps and Priorities

High-Priority Gaps

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

Medium-Priority Gaps

Non-neuronal cells: Vascular, meningeal, lymphatic

Subcortical structures: Thalamus, hypothalamus

Aging time course: Cross-sectional vs. longitudinal

Emerging Priorities

Multi-omics integration: Transcriptomics + proteomics + epigenomics

Cellular trajectories: Development and disease progression

Circuit integration: Single-cell + connectomics

Data Access

[Alzheimer's Disease](/diseases/alzheimers-disease)
[Parkinson's Disease](/diseases/parkinsons-disease)

External Links

[PubMed](https://pubmed.ncbi.nlm.nih.gov/)
[KEGG Pathways](https://www.genome.jp/kegg/pathway.html)

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cell-types-cell-atlas-coverage

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slug	cell-types-cell-atlas-coverage
kg_node_id	None
entity_type	cell
origin_type	v1_polymorphic_backfill
source_table	wiki_pages
wiki_page_id	wp-05675fb31787
__merged_from	{'merged_at': '2026-05-13', 'unprefixed_id': 'cell-types-cell-atlas-coverage'}
_schema_version	1

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