Human Brain Cell Atlas v1.0
A first draft atlas of human brain transcriptomic cell typesAtlas Description
The human brain directs a wide range of complex behaviors ranging from fine motor skills to abstract intelligence and emotion. This broad range of functions is supported by an exceptionally complex cellular and circuit architecture. To create a first draft human brain cell atlas, high-throughput single-nucleus RNA sequencing was used to systematically survey cells across the entire adult human brain in three postmortem donors. Over three million nuclei were sampled from approximately 100 dissections across the forebrain, midbrain, and hindbrain. Analysis of these data showed regional diversity in cellular organization at multiple scales, identifying 30 superclusters, 461 clusters, and 3313 subclusters. As the first single-cell transcriptomic census of the entire human brain, this atlas provides a resource for understanding the molecular diversity of the human brain in health and disease.
The Human Brain Cell Atlas v1.0 is presented for visualization and data mining through the Chan Zuckerberg Initiative’s CELLxGENE application, with the following biologically meaningful partitions:
- Neuronal and non-neuronal cell types
- Supercluster-specific groupings
- Brain region-specific groupings, ordered by the adult human brain anatomical reference atlas ontology in Ding et al. (2016)
| Atlas Name | Tissue | Disease | Cells | Explore | Download |
|---|---|---|---|---|---|
All neurons | 10 tissues | normal | 2.5M | ||
All non-neuronal cells | 10 tissues | normal | 888.3k | ||
Supercluster: Oligodendrocyte | 10 tissues | normal | 490.2k | ||
Supercluster: Upper-layer intratelencephalic | 9 tissues | normal | 455.0k | ||
Supercluster: Splatter | 10 tissues | normal | 291.8k | ||
Supercluster: Deep-layer intratelencephalic | 8 tissues | normal | 228.5k | ||
Supercluster: CGE interneuron | 9 tissues | normal | 227.7k | ||
Supercluster: MGE interneuron | 9 tissues | normal | 222.4k | ||
Supercluster: Astrocyte | 10 tissues | normal | 155.0k | ||
Supercluster: Medium spiny neuron | 7 tissues | normal | 152.2k | ||
Supercluster: Upper rhombic lip | 10 tissues | normal | 137.2k | ||
Supercluster: Midbrain-derived inhibitory | 10 tissues | normal | 126.8k | ||
Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C | cerebral cortex | normal | 116.6k | ||
Supercluster: Amygdala excitatory | 7 tissues | normal | 109.5k | ||
Dissection: Cerebral cortex (Cx) - Middle Temporal Gyrus - MTG | cerebral cortex | normal | 107.3k | ||
Supercluster: Oligodendrocyte precursor | 10 tissues | normal | 105.7k | ||
Supercluster: Microglia | 10 tissues | normal | 91.8k | ||
Supercluster: Thalamic excitatory | 6 tissues | normal | 85.5k | ||
Supercluster: Deep-layer corticothalamic and 6b | 6 tissues | normal | 78.4k | ||
Supercluster: Hippocampal CA1-3 | 6 tissues | normal | 75.0k | ||
Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV | cerebellum | normal | 71.9k | ||
Supercluster: Hippocampal dentate gyrus | 4 tissues | normal | 67.5k | ||
Dissection: Midbrain (M) - Substantia Nigra - SN | midbrain | normal | 59.5k | ||
Dissection: Tail of Hippocampus (HiT) - Caudal Hippocampus - CA4-DGC | hippocampal formation | normal | 56.4k | ||
Supercluster: Lower rhombic lip | 8 tissues | normal | 52.6k | ||
Dissection: Cerebellum (CB) - Cerebellar deep nuclei - CbDN | cerebellum | normal | 52.0k | ||
Dissection: Basal nuclei (BN) - Globus pallidus (GP) - External segment of globus pallidus - GPe | cerebral nuclei | normal | 50.8k | ||
Dissection: Cerebral cortex (Cx) - Anterior parahippocampal gyrus, posterior part (APH) - Medial entorhinal cortex - MEC | cerebral cortex | normal | 50.4k | ||
Dissection: Pons (Pn) - Pontine reticular formation - PnRF | pons | normal | 49.5k | ||
Dissection: Midbrain (M) - Substantia Nigra, Red Nucleus, and nearby nuclei - SN-RN | midbrain | normal | 49.1k | ||
Dissection: Thalamus (THM) - posterior nuclear complex of thalamus (PoN) - lateral geniculate nucleus (LG) | thalamic complex | normal | 48.9k | ||
Dissection: Pons (Pn) - efferent nuclei of cranial nerves in pons - PnEN | pons | normal | 47.4k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - Pulvinar of thalamus - Pul | thalamic complex | normal | 46.5k | ||
Supercluster: LAMP5-LHX6 and Chandelier | 8 tissues | normal | 45.1k | ||
Dissection: Cerebral cortex (Cx) - Parietal operculum (PaO) - Gustatory cortex - A43 | cerebral cortex | normal | 42.8k | ||
Dissection: Amygdaloid complex (AMY) - Central nuclear group - CEN | cerebral nuclei | normal | 42.7k | ||
Dissection: Head of hippocampus (HiH) - Tail of Hippocampus (HiT) - Subicular cortex - Sub | hippocampal formation | normal | 41.6k | ||
Dissection: Basal forebrain (BF) - septal nuclei - SEP | cerebral nuclei | normal | 40.8k | ||
Dissection: Cerebral cortex (Cx) - Posterior parahippocampal gyrus (PPH) - TH-TL | cerebral cortex | normal | 40.7k | ||
Dissection: Cerebral cortex (Cx) - Superior Temporal Gyrus - STG | cerebral cortex | normal | 40.6k | ||
Dissection: Body of hippocampus (HiB) - Rostral DG-CA4 | hippocampal formation | normal | 40.2k | ||
Dissection: Claustrum - Cla | cerebral nuclei | normal | 40.2k | ||
Supercluster: Eccentric medium spiny neuron | 6 tissues | normal | 40.1k | ||
Dissection: Cerebral cortex (Cx) - Long insular gyri (LIG) - Dysgranular insular cortex - Idg | cerebral cortex | normal | 39.7k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA1 | hippocampal formation | normal | 39.1k | ||
Dissection: Cerebral cortex (Cx) - Supramarginal gyrus (SMG) - A40 | cerebral cortex | normal | 39.1k | ||
Dissection: Cerebral cortex (Cx) - Short insular gyri - Granular insular cortex - Ig | cerebral cortex | normal | 38.9k | ||
Dissection: Amygdaloid complex (AMY) - corticomedial nuclear group - CMN | cerebral nuclei | normal | 38.3k | ||
Dissection: Cerebral cortex (Cx) - Inferior frontal gyrus (IFG) - Ventrolateral prefrontal cortex - A44-A45 | cerebral cortex | normal | 38.3k | ||
Dissection: Basal forebrain (BF) - substantia innominata and nearby nuclei - SI | cerebral nuclei | normal | 38.2k | ||
Dissection: Cerebral cortex (Cx) - Postcentral gyrus (PoCG) - Primary somatosensory cortex - S1C | cerebral cortex | normal | 38.2k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA1-CA3 | hippocampal formation | normal | 37.9k | ||
Dissection: Cerebral cortex (Cx) - Subcallosal Gyrus (SCG) - Subgenual (subcallosal) division of MFC - A25 | cerebral cortex | normal | 37.8k | ||
Dissection: Cerebral cortex (Cx) - Temporal pole (TP) - Temporopolar area - A38 | cerebral cortex | normal | 37.6k | ||
Dissection: Paleocortex (PalCx) - Piriform cortex - Pir | cerebral cortex | normal | 36.9k | ||
Dissection: Tail of Hippocampus (HiT) - Caudal Hippocampus - CA1-CA3 | hippocampal formation | normal | 36.9k | ||
Dissection: Cerebral cortex (Cx) - Caudal cingulate gyrus (CgGC) - A23 | cerebral cortex | normal | 35.4k | ||
Dissection: Head of hippocampus (HiH) - Uncal DG-CA4 | hippocampal formation | normal | 35.4k | ||
Dissection: Cerebral cortex (Cx) - Supraparietal lobule (SPL) - Posterosuperior (dorsal) parietal cortex - A5-A7 | cerebral cortex | normal | 35.3k | ||
Dissection: Amygdaloid complex (AMY) - basolateral nuclear group (BLN) - basolateral nucleus (basal nucleus) - BL | cerebral nuclei | normal | 35.3k | ||
Dissection: Cerebral cortex (Cx) - Frontal agranular insular cortex - FI | cerebral cortex | normal | 34.9k | ||
Dissection: Extended amygdala (EXA) - Bed nucleus of stria terminalis and nearby - BNST | cerebral nuclei | normal | 34.9k | ||
Dissection: Cerebral cortex (Cx) - Posterior intermediate orbital gyrus (POrG) - Caudal division of OFCi - A13 | cerebral cortex | normal | 34.9k | ||
Dissection: Basal nuclei (BN) - Putamen - Pu | cerebral nuclei | normal | 34.4k | ||
Dissection: Cerebral cortex (Cx) - Cingulate gyrus, retrosplenial (CgGrs) - A29-A30 | cerebral cortex | normal | 34.1k | ||
Dissection: Basal nuclei (BN) - Globus pallidus (GP) - Internal segment of globus pallidus - GPi | cerebral nuclei | normal | 34.0k | ||
Dissection: Midbrain (M) - Periaqueductal gray and nearby nuclei - PAG | midbrain | normal | 33.8k | ||
Dissection: Pons (Pn) - Pontine Nucleus - PN | pons | normal | 33.6k | ||
Dissection: Cerebral cortex (Cx) - Lingual gyrus (LiG) - Primary Visual Cortex - V1C | cerebral cortex | normal | 33.5k | ||
Dissection: Cerebral cortex (Cx) - Transverse temporal gyrus (TTG) - Primary auditory cortex - A1C | cerebral cortex | normal | 32.8k | ||
Dissection: Cerebral cortex (Cx) - Anterior parahippocampal gyrus (AG) - Lateral entorhinal cortex - LEC | cerebral cortex | normal | 32.7k | ||
Dissection: Basal nuclei (BN) - Body of the Caudate - CaB | cerebral nuclei | normal | 32.7k | ||
Dissection: Cerebral cortex (Cx) - Cuneus, caudal part - Peristriate Cortex - V2 | cerebral cortex | normal | 32.6k | ||
Dissection: Midbrain (M) - Inferior colliculus and nearby nuclei - IC | midbrain | normal | 32.3k | ||
Dissection: Cerebral cortex (Cx) - Cingulate gyrus, rostral (CgGr) - Ventral division of MFC - A24 | cerebral cortex | normal | 32.2k | ||
Dissection: Cerebral cortex (Cx) - Occipitotemporal (fusiform) gyrus, temporal part (FuGt) - Temporal area TF | cerebral cortex | normal | 31.9k | ||
Dissection: Thalamus (THM) - Anterior nuclear complex - ANC | thalamic complex | normal | 31.3k | ||
Dissection: Paleocortex (PalCx) - Anterior Olfactory Nucleus - AON | cerebral cortex | normal | 31.2k | ||
Dissection: Amygdaloid complex (AMY) - basolateral nuclear group (BLN) - basomedial nucleus (accessory basal nucleus) - BM | cerebral nuclei | normal | 31.1k | ||
Dissection: Cerebral cortex (Cx) - Middle frontal gyrus (MFG) - A46 | cerebral cortex | normal | 31.1k | ||
Dissection: Basal nuclei (BN) - Nucleus Accumbens - NAC | cerebral nuclei | normal | 30.1k | ||
Dissection: Midbrain (M) - Superior colliculus and nearby nuclei - SC | midbrain | normal | 29.9k | ||
Dissection: Cerebral cortex (Cx) - Superior occipital gyrus (SOG) - Areas 19 and MT - A19 | cerebral cortex | normal | 29.7k | ||
Dissection: Cerebral cortex (Cx) - Inferior temporal gyrus - ITG | cerebral cortex | normal | 29.5k | ||
Dissection: Amygdaloid complex (AMY) - Basolateral nuclear group (BLN) - lateral nucleus - La | cerebral nuclei | normal | 29.0k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA1-CA3 | hippocampal formation | normal | 28.7k | ||
Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) - mammillary nucleus - MN | hypothalamus | normal | 28.2k | ||
Dissection: Cerebral cortex (Cx) - Cuneus, rostral part - Area Prostriata - Pro | cerebral cortex | normal | 28.1k | ||
Dissection: Cerebellum (CB) - Lateral hemisphere of cerebellum - CBL | cerebellum | normal | 28.0k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - afferent nuclei of cranial nerves in medulla oblongata - MoAN | myelencephalon | normal | 27.2k | ||
Dissection: Thalamus (THM) - Lateral nuclear complex of thalamus (LNC) - ventral group of lateral nucleus - VLN | thalamic complex | normal | 27.1k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - lateral posterior nucleus of thalamus - LP | thalamic complex | normal | 26.2k | ||
Dissection: Pons (Pn) - other nuclei in pontine tegmentum (XPnTg) - dorsal tegmental nucleus - DTg | pons | normal | 26.1k | ||
Dissection: Midbrain (M) - Pretectal region - PTR | midbrain | normal | 25.9k | ||
Supercluster: Miscellaneous | 10 tissues | normal | 25.1k | ||
Dissection: Cerebral cortex (Cx) - Rostral gyrus (RoG) - Dorsal division of MFC - A32 | cerebral cortex | normal | 24.8k | ||
Dissection: Thalamus (THM) - intralaminar nuclear complex (ILN) - posterior group of intralaminar nuclei (PILN) - centromedian and parafasicular nuclei - CM and Pf | thalamic complex | normal | 24.4k | ||
Dissection: Epithalamus - ETH | thalamic complex | normal | 24.3k | ||
Dissection: Spinal cord - SpC | spinal cord | normal | 24.2k | ||
Dissection: Pons (Pn) - Pontine reticular formation (PnRF) - parabrachial nuclei - PB | pons | normal | 24.2k | ||
Dissection: Cerebral cortex (Cx) - Perirhinal gyrus (PRG) - A35-A36 | cerebral cortex | normal | 23.7k | ||
Dissection: Pons (Pn) - afferent nuclei of cranial nerves in pons - PnAN | pons | normal | 23.3k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - medullary reticular formation (MoRF) & efferent nuclei of cranial nerves in the medulla oblongata (MoEN) - MoRF-MoEN | myelencephalon | normal | 23.1k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - precerebellar nuclei (PrCbN) - inferior olive - IO | myelencephalon | normal | 21.5k | ||
Dissection: Thalamus (THM) - medial nuclear complex of thalamus (MNC) - mediodorsal nucleus of thalamus - MD | thalamic complex | normal | 20.9k | ||
Dissection: Thalamus (THM) - Subthalamic nucleus and nearby - STH | thalamic complex | normal | 20.2k | ||
Dissection: Hypothalamus (HTH) - preoptic region of HTH - HTHpo (medial preoptic nucleus, MPN) - supraoptic region of HTH - HTHso (paraventricular nucleus, PV) | hypothalamus | normal | 20.0k | ||
Supercluster: Deep-layer near-projecting | 6 tissues | normal | 18.9k | ||
Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) - tuberal region of HTH - HTHtub | hypothalamus | normal | 18.7k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - lateral posterior nucleus of thalamus + ventral posterior lateral nucleus - LP + VPL | thalamic complex | normal | 17.7k | ||
Dissection: Perirhinal cortex (area 35) (A35) - rostral subdivision of area 35 - A35r | cerebral cortex | normal | 17.5k | ||
Dissection: Hypothalamus (HTH) - supraoptic region of HTH - HTHso (anterior hypothalamic nucleus, AHN) - tuberal region of HTH - HTHtub (ventromedial and dorsomedial hypothalamic nucleic nuclei, VMH, DMH) | hypothalamus | normal | 16.8k | ||
Supercluster: Mammillary body | 5 tissues | normal | 16.6k | ||
Dissection: Hypothalamus (HTH) - preoptic region of HTH - HTHpo | hypothalamus | normal | 15.0k | ||
Supercluster: Cerebellar inhibitory | 9 tissues | normal | 14.4k | ||
Dissection: Cerebral cortex (Cx) - Gyrus rectus (ReG) - Medial orbitofrontal cortex - A14 | cerebral cortex | normal | 14.4k | ||
Dissection: Thalamus (THM) - posterior nuclear complex of thalamus (PoN) - medial geniculate nuclei (MG) | thalamic complex | normal | 14.2k | ||
Dissection: Midbrain (M) - Periaqueductal gray and Dorsal raphe nucleus - PAG-DR | midbrain | normal | 14.1k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR | myelencephalon | normal | 13.6k | ||
Dissection: Thalamus (THM) - medial nuclear complex of thalamus (MNC) - mediodorsal nucleus of thalamus + reuniens nucleus (medioventral nucleus) of thalamus - MD + Re | thalamic complex | normal | 13.4k | ||
Dissection: Hypothalamus (HTH) - tuberal region of hypothalamus - HTHtub | hypothalamus | normal | 13.2k | ||
Dissection: Thalamus (THM) - intralaminar nuclear complex (ILN) - posterior group of intralaminar nuclei (PILN) - centromedian nucleus of thalamus - CM | thalamic complex | normal | 12.9k | ||
Dissection: Hypothalamus (HTH) - supraoptic region of HTH - HTHso | hypothalamus | normal | 12.6k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA2-CA3 | hippocampal formation | normal | 12.5k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA1-2 | hippocampal formation | normal | 11.3k | ||
Dissection: Amygdaloid complex (AMY) - Corticomedial nuclear group (CMN) - anterior cortical nucleus - CoA | cerebral nuclei | normal | 10.8k | ||
Supercluster: Hippocampal CA4 | 5 tissues | normal | 10.7k | ||
Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) | hypothalamus | normal | 10.1k | ||
Supercluster: Vascular | 10 tissues | normal | 9.9k | ||
Supercluster: Fibroblast | 10 tissues | normal | 9.2k | ||
Dissection: Thalamus (THM) - Lateral nuclear complex (LNC) - ventral anterior nucleus of thalamus - VA | thalamic complex | normal | 8.6k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA3 | hippocampal formation | normal | 8.1k | ||
Supercluster: Bergmann glia | 8 tissues | normal | 8.0k | ||
Supercluster: Choroid plexus | 10 tissues | normal | 7.7k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - ventral posterior lateral nucleus - VPL | thalamic complex | normal | 6.9k | ||
Supercluster: Ependymal | 10 tissues | normal | 5.9k | ||
Supercluster: Committed oligodendrocyte precursor | 10 tissues | normal | 4.7k | ||
Dissection: Midbrain (RN) - Red Nucleus - RN | midbrain | normal | 4.7k |
