<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]