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 | 88 tissues | normal | 2.5M | ||
All non-neuronal cells | 88 tissues | normal | 888.3k | ||
Supercluster: Oligodendrocyte | 88 tissues | normal | 490.2k | ||
Supercluster: Upper-layer intratelencephalic | 80 tissues | normal | 455.0k | ||
Supercluster: Splatter | 87 tissues | normal | 291.8k | ||
Supercluster: Deep-layer intratelencephalic | 68 tissues | normal | 228.5k | ||
Supercluster: CGE interneuron | 84 tissues | normal | 227.7k | ||
Supercluster: MGE interneuron | 80 tissues | normal | 222.4k | ||
Supercluster: Astrocyte | 88 tissues | normal | 155.0k | ||
Supercluster: Medium spiny neuron | 45 tissues | normal | 152.2k | ||
Supercluster: Upper rhombic lip | 48 tissues | normal | 137.2k | ||
Supercluster: Midbrain-derived inhibitory | 45 tissues | normal | 126.8k | ||
Dissection: Cerebral cortex (Cx) - Precentral gyrus (PrCG) - Primary motor cortex - M1C | primary motor cortex | normal | 116.6k | ||
Supercluster: Amygdala excitatory | 52 tissues | normal | 109.5k | ||
Dissection: Cerebral cortex (Cx) - Middle Temporal Gyrus - MTG | middle temporal gyrus | normal | 107.3k | ||
Supercluster: Oligodendrocyte precursor | 88 tissues | normal | 105.7k | ||
Supercluster: Microglia | 88 tissues | normal | 91.8k | ||
Supercluster: Thalamic excitatory | 28 tissues | normal | 85.5k | ||
Supercluster: Deep-layer corticothalamic and 6b | 64 tissues | normal | 78.4k | ||
Supercluster: Hippocampal CA1-3 | 29 tissues | normal | 75.0k | ||
Dissection: Cerebellum (CB) - Cerebellar Vermis - CBV | cerebellar vermis | normal | 71.9k | ||
Supercluster: Hippocampal dentate gyrus | 12 tissues | normal | 67.5k | ||
Dissection: Midbrain (M) - Substantia Nigra - SN | substantia nigra | normal | 59.5k | ||
Dissection: Tail of Hippocampus (HiT) - Caudal Hippocampus - CA4-DGC | dentate gyrus of hippocampal formation | normal | 56.4k | ||
Supercluster: Lower rhombic lip | 18 tissues | normal | 52.6k | ||
Dissection: Cerebellum (CB) - Cerebellar deep nuclei - CbDN | cerebellar nuclear complex | normal | 52.0k | ||
Dissection: Basal nuclei (BN) - Globus pallidus (GP) - External segment of globus pallidus - GPe | globus pallidus | normal | 50.8k | ||
Dissection: Cerebral cortex (Cx) - Anterior parahippocampal gyrus, posterior part (APH) - Medial entorhinal cortex - MEC | medial entorhinal cortex | normal | 50.4k | ||
Dissection: Pons (Pn) - Pontine reticular formation - PnRF | pontine reticular formation | normal | 49.5k | ||
Dissection: Midbrain (M) - Substantia Nigra, Red Nucleus, and nearby nuclei - SN-RN | midbrain nucleus | normal | 49.1k | ||
Dissection: Thalamus (THM) - posterior nuclear complex of thalamus (PoN) - lateral geniculate nucleus (LG) | lateral geniculate body | normal | 48.9k | ||
Dissection: Pons (Pn) - efferent nuclei of cranial nerves in pons - PnEN | pontine tegmentum | normal | 47.4k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - Pulvinar of thalamus - Pul | pulvinar nucleus | normal | 46.5k | ||
Supercluster: LAMP5-LHX6 and Chandelier | 79 tissues | normal | 45.1k | ||
Dissection: Cerebral cortex (Cx) - Parietal operculum (PaO) - Gustatory cortex - A43 | Brodmann (1909) area 43 | normal | 42.8k | ||
Dissection: Amygdaloid complex (AMY) - Central nuclear group - CEN | central amygdaloid nucleus | normal | 42.7k | ||
Dissection: Head of hippocampus (HiH) - Tail of Hippocampus (HiT) - Subicular cortex - Sub | subicular complex | normal | 41.6k | ||
Dissection: Basal forebrain (BF) - septal nuclei - SEP | septal nuclear complex | normal | 40.8k | ||
Dissection: Cerebral cortex (Cx) - Posterior parahippocampal gyrus (PPH) - TH-TL | posterior parahippocampal gyrus | normal | 40.7k | ||
Dissection: Cerebral cortex (Cx) - Superior Temporal Gyrus - STG | superior temporal gyrus | normal | 40.6k | ||
Dissection: Body of hippocampus (HiB) - Rostral DG-CA4 | dentate gyrus of hippocampal formation | normal | 40.2k | ||
Dissection: Claustrum - Cla | claustrum of brain | normal | 40.2k | ||
Supercluster: Eccentric medium spiny neuron | 47 tissues | normal | 40.1k | ||
Dissection: Cerebral cortex (Cx) - Long insular gyri (LIG) - Dysgranular insular cortex - Idg | agranular insular cortex | normal | 39.7k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA1 | uncal CA1 | normal | 39.1k | ||
Dissection: Cerebral cortex (Cx) - Supramarginal gyrus (SMG) - A40 | Brodmann (1909) area 40 | normal | 39.1k | ||
Dissection: Cerebral cortex (Cx) - Short insular gyri - Granular insular cortex - Ig | granular insular cortex | normal | 38.9k | ||
Dissection: Amygdaloid complex (AMY) - corticomedial nuclear group - CMN | corticomedial nuclear complex | normal | 38.3k | ||
Dissection: Cerebral cortex (Cx) - Inferior frontal gyrus (IFG) - Ventrolateral prefrontal cortex - A44-A45 | inferior frontal gyrus | normal | 38.3k | ||
Dissection: Basal forebrain (BF) - substantia innominata and nearby nuclei - SI | substantia innominata | normal | 38.2k | ||
Dissection: Cerebral cortex (Cx) - Postcentral gyrus (PoCG) - Primary somatosensory cortex - S1C | primary somatosensory cortex | normal | 38.2k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA1-CA3 | hippocampal field | normal | 37.9k | ||
Dissection: Cerebral cortex (Cx) - Subcallosal Gyrus (SCG) - Subgenual (subcallosal) division of MFC - A25 | Brodmann (1909) area 25 | normal | 37.8k | ||
Dissection: Cerebral cortex (Cx) - Temporal pole (TP) - Temporopolar area - A38 | Brodmann (1909) area 38 | normal | 37.6k | ||
Dissection: Paleocortex (PalCx) - Piriform cortex - Pir | piriform cortex | normal | 36.9k | ||
Dissection: Tail of Hippocampus (HiT) - Caudal Hippocampus - CA1-CA3 | hippocampal field | normal | 36.9k | ||
Dissection: Cerebral cortex (Cx) - Caudal cingulate gyrus (CgGC) - A23 | Brodmann (1909) area 23 | normal | 35.4k | ||
Dissection: Head of hippocampus (HiH) - Uncal DG-CA4 | dentate gyrus of hippocampal formation | normal | 35.4k | ||
Dissection: Cerebral cortex (Cx) - Supraparietal lobule (SPL) - Posterosuperior (dorsal) parietal cortex - A5-A7 | superior parietal cortex | normal | 35.3k | ||
Dissection: Amygdaloid complex (AMY) - basolateral nuclear group (BLN) - basolateral nucleus (basal nucleus) - BL | basolateral amygdaloid nuclear complex | normal | 35.3k | ||
Dissection: Cerebral cortex (Cx) - Frontal agranular insular cortex - FI | agranular insular cortex | normal | 34.9k | ||
Dissection: Extended amygdala (EXA) - Bed nucleus of stria terminalis and nearby - BNST | bed nucleus of stria terminalis | normal | 34.9k | ||
Dissection: Cerebral cortex (Cx) - Posterior intermediate orbital gyrus (POrG) - Caudal division of OFCi - A13 | Brodmann (1909) area 13 | normal | 34.9k | ||
Dissection: Basal nuclei (BN) - Putamen - Pu | putamen | normal | 34.4k | ||
Dissection: Cerebral cortex (Cx) - Cingulate gyrus, retrosplenial (CgGrs) - A29-A30 | retrosplenial region | normal | 34.1k | ||
Dissection: Basal nuclei (BN) - Globus pallidus (GP) - Internal segment of globus pallidus - GPi | globus pallidus | normal | 34.0k | ||
Dissection: Midbrain (M) - Periaqueductal gray and nearby nuclei - PAG | gray matter of midbrain | normal | 33.8k | ||
Dissection: Pons (Pn) - Pontine Nucleus - PN | pontine nuclear group | normal | 33.6k | ||
Dissection: Cerebral cortex (Cx) - Lingual gyrus (LiG) - Primary Visual Cortex - V1C | primary visual cortex | normal | 33.5k | ||
Dissection: Cerebral cortex (Cx) - Transverse temporal gyrus (TTG) - Primary auditory cortex - A1C | primary auditory cortex | normal | 32.8k | ||
Dissection: Cerebral cortex (Cx) - Anterior parahippocampal gyrus (AG) - Lateral entorhinal cortex - LEC | lateral entorhinal cortex | normal | 32.7k | ||
Dissection: Basal nuclei (BN) - Body of the Caudate - CaB | body of caudate nucleus | normal | 32.7k | ||
Dissection: Cerebral cortex (Cx) - Cuneus, caudal part - Peristriate Cortex - V2 | extrastriate cortex | normal | 32.6k | ||
Dissection: Midbrain (M) - Inferior colliculus and nearby nuclei - IC | midbrain tectum | normal | 32.3k | ||
Dissection: Cerebral cortex (Cx) - Cingulate gyrus, rostral (CgGr) - Ventral division of MFC - A24 | Brodmann (1909) area 24 | normal | 32.2k | ||
Dissection: Cerebral cortex (Cx) - Occipitotemporal (fusiform) gyrus, temporal part (FuGt) - Temporal area TF | temporal fusiform gyrus | normal | 31.9k | ||
Dissection: Thalamus (THM) - Anterior nuclear complex - ANC | anterior nuclear group | normal | 31.3k | ||
Dissection: Paleocortex (PalCx) - Anterior Olfactory Nucleus - AON | anterior olfactory nucleus | normal | 31.2k | ||
Dissection: Amygdaloid complex (AMY) - basolateral nuclear group (BLN) - basomedial nucleus (accessory basal nucleus) - BM | accessory basal amygdaloid nucleus | normal | 31.1k | ||
Dissection: Cerebral cortex (Cx) - Middle frontal gyrus (MFG) - A46 | Brodmann (1909) area 46 | normal | 31.1k | ||
Dissection: Basal nuclei (BN) - Nucleus Accumbens - NAC | nucleus accumbens | normal | 30.1k | ||
Dissection: Midbrain (M) - Superior colliculus and nearby nuclei - SC | midbrain tectum | normal | 29.9k | ||
Dissection: Cerebral cortex (Cx) - Superior occipital gyrus (SOG) - Areas 19 and MT - A19 | Brodmann (1909) area 19 | normal | 29.7k | ||
Dissection: Cerebral cortex (Cx) - Inferior temporal gyrus - ITG | inferior temporal gyrus | normal | 29.5k | ||
Dissection: Amygdaloid complex (AMY) - Basolateral nuclear group (BLN) - lateral nucleus - La | lateral amygdaloid nucleus | normal | 29.0k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA1-CA3 | hippocampal field | normal | 28.7k | ||
Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) - mammillary nucleus - MN | mammillary body | normal | 28.2k | ||
Dissection: Cerebral cortex (Cx) - Cuneus, rostral part - Area Prostriata - Pro | cuneus cortex | normal | 28.1k | ||
Dissection: Cerebellum (CB) - Lateral hemisphere of cerebellum - CBL | cerebrocerebellum | normal | 28.0k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - afferent nuclei of cranial nerves in medulla oblongata - MoAN | nucleus of medulla oblongata | normal | 27.2k | ||
Dissection: Thalamus (THM) - Lateral nuclear complex of thalamus (LNC) - ventral group of lateral nucleus - VLN | lateral nuclear group of thalamus | normal | 27.1k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - lateral posterior nucleus of thalamus - LP | lateral posterior nucleus of thalamus | normal | 26.2k | ||
Dissection: Pons (Pn) - other nuclei in pontine tegmentum (XPnTg) - dorsal tegmental nucleus - DTg | dorsal tegmental nucleus | normal | 26.1k | ||
Dissection: Midbrain (M) - Pretectal region - PTR | pretectal region | normal | 25.9k | ||
Supercluster: Miscellaneous | 88 tissues | normal | 25.1k | ||
Dissection: Cerebral cortex (Cx) - Rostral gyrus (RoG) - Dorsal division of MFC - A32 | 2 tissues | normal | 24.8k | ||
Dissection: Thalamus (THM) - intralaminar nuclear complex (ILN) - posterior group of intralaminar nuclei (PILN) - centromedian and parafasicular nuclei - CM and Pf | intralaminar nuclear group | normal | 24.4k | ||
Dissection: Epithalamus - ETH | epithalamus | normal | 24.3k | ||
Dissection: Spinal cord - SpC | spinal cord | normal | 24.2k | ||
Dissection: Pons (Pn) - Pontine reticular formation (PnRF) - parabrachial nuclei - PB | parabrachial nucleus | normal | 24.2k | ||
Dissection: Cerebral cortex (Cx) - Perirhinal gyrus (PRG) - A35-A36 | perirhinal cortex | normal | 23.7k | ||
Dissection: Pons (Pn) - afferent nuclei of cranial nerves in pons - PnAN | pontine tegmentum | normal | 23.3k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - medullary reticular formation (MoRF) & efferent nuclei of cranial nerves in the medulla oblongata (MoEN) - MoRF-MoEN | nucleus of medulla oblongata | normal | 23.1k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - precerebellar nuclei (PrCbN) - inferior olive - IO | inferior olivary complex | normal | 21.5k | ||
Dissection: Thalamus (THM) - medial nuclear complex of thalamus (MNC) - mediodorsal nucleus of thalamus - MD | medial dorsal nucleus of thalamus | normal | 20.9k | ||
Dissection: Thalamus (THM) - Subthalamic nucleus and nearby - STH | subthalamic nucleus | 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 | 48 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 | nucleus of dorsal thalamus | normal | 17.7k | ||
Dissection: Perirhinal cortex (area 35) (A35) - rostral subdivision of area 35 - A35r | Brodmann (1909) area 35 | 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 | 11 tissues | normal | 16.6k | ||
Dissection: Hypothalamus (HTH) - preoptic region of HTH - HTHpo | preoptic area | normal | 15.0k | ||
Supercluster: Cerebellar inhibitory | 30 tissues | normal | 14.4k | ||
Dissection: Cerebral cortex (Cx) - Gyrus rectus (ReG) - Medial orbitofrontal cortex - A14 | Brodmann (1909) area 14 | normal | 14.4k | ||
Dissection: Thalamus (THM) - posterior nuclear complex of thalamus (PoN) - medial geniculate nuclei (MG) | medial geniculate body | normal | 14.2k | ||
Dissection: Midbrain (M) - Periaqueductal gray and Dorsal raphe nucleus - PAG-DR | gray matter of midbrain | normal | 14.1k | ||
Dissection: Myelencephalon (medulla oblongata) (Mo) - sensory relay nuclei in medulla oblongata - MoSR | nucleus of medulla oblongata | normal | 13.6k | ||
Dissection: Thalamus (THM) - medial nuclear complex of thalamus (MNC) - mediodorsal nucleus of thalamus + reuniens nucleus (medioventral nucleus) of thalamus - MD + Re | nucleus of dorsal thalamus | normal | 13.4k | ||
Dissection: Hypothalamus (HTH) - tuberal region of hypothalamus - HTHtub | median tuberal portion | normal | 13.2k | ||
Dissection: Thalamus (THM) - intralaminar nuclear complex (ILN) - posterior group of intralaminar nuclei (PILN) - centromedian nucleus of thalamus - CM | centromedian nucleus of thalamus | normal | 12.9k | ||
Dissection: Hypothalamus (HTH) - supraoptic region of HTH - HTHso | supraoptic nucleus | normal | 12.6k | ||
Dissection: Head of hippocampus (HiH) - Uncal CA2-CA3 | hippocampal field | normal | 12.5k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA1-2 | hippocampal field | normal | 11.3k | ||
Dissection: Amygdaloid complex (AMY) - Corticomedial nuclear group (CMN) - anterior cortical nucleus - CoA | anterior cortical amygdaloid nucleus | normal | 10.8k | ||
Supercluster: Hippocampal CA4 | 10 tissues | normal | 10.7k | ||
Dissection: Hypothalamus (HTH) - mammillary region of HTH (HTHma) | medial zone of hypothalamus | normal | 10.1k | ||
Supercluster: Vascular | 88 tissues | normal | 9.9k | ||
Supercluster: Fibroblast | 88 tissues | normal | 9.2k | ||
Dissection: Thalamus (THM) - Lateral nuclear complex (LNC) - ventral anterior nucleus of thalamus - VA | ventral anterior nucleus of thalamus | normal | 8.6k | ||
Dissection: Body of hippocampus (HiB) - Rostral CA3 | rostral CA3 | normal | 8.1k | ||
Supercluster: Bergmann glia | 16 tissues | normal | 8.0k | ||
Supercluster: Choroid plexus | 20 tissues | normal | 7.7k | ||
Dissection: Thalamus (THM) - lateral nuclear complex of thalamus (LNC) - ventral posterior lateral nucleus - VPL | lateral posterior nucleus of thalamus | normal | 6.9k | ||
Supercluster: Ependymal | 45 tissues | normal | 5.9k | ||
Supercluster: Committed oligodendrocyte precursor | 88 tissues | normal | 4.7k | ||
Dissection: Midbrain (RN) - Red Nucleus - RN | red nucleus | normal | 4.7k |
