The single nuclei brain - Explore the expression profiles in single nuclei brain cell types

Single nuclei brain methods

This resource provides brain cell type expression profiles based on single-nucleus RNA sequencing (snRNA-seq) data, covering 11 brain regions and approximately 2.5 million nuclei. The analysis is based on genome-wide expression data published by Siletti K et al. (2023), comprising over 3 million cells from across the human brain.

For the Human Protein Atlas, the data were reprocessed, with neuronal and non-neuronal cells clustered separately. The resulting cell type clusters were annotated and organized into 48 main cell types, providing a detailed overview of cellular diversity across brain regions. Genes were classified according to their expression specificity across cell types, identifying genes with elevated expression in particular cell populations. The distribution of these specificity categories is presented in the pie chart and tables below.

The integration of this extensive brain snRNA-seq dataset enables exploration of regional differences in cell type expression and facilitates comparisons with other datasets. The Single cell type resource provides a complementary whole-body perspective, integrating cell type expression profiles from peripheral tissues with a selected subset of the brain snRNA-seq data.

More information about the datasets, processing, and analytical methods can be found in the Methods Summary, and in data details.

Learn about:

RNA expression profiles across neuronal and non-neuronal cell types in the human brain
Genes with elevated or enriched expression in specific brain cell types
Regional differences in gene expression across brain cell populations
Expression patterns of individual genes across brain regions and cell types

SINGLE NUCLEI BRAIN REGIONⁱ

Classification of all protein-coding genes based on single cell type-specific expression, determining the number of genes elevated (cell type/group enriched, cell type enhanced) in a particular cell type compared to all other cell types.

Interactive table with numbers of genes classified as elevated for each main cell type. Neurons are here grouped into broad categories for a better comparison with the non-neuronal cells of the brain. A more detailed within neuron- category is also calculated and described further in the Neuron summary page.

Cell type group	Cell type	Enriched	Group enriched	Enhanced	Total elevated
Neuronal cells	Inhibitory	199	659	573	1431
	Excitatory	108	684	582	1374
	Specialized neurotransmitter neurons	72	461	208	741
	Neurosecretory	6	184	43	233
	Other Neuron	14	297	71	382
Glial cells	Astrocytes	19	148	128	295
	Bergmann glia	15	111	126	252
Ciliated cells	Ependymal cells	170	239	262	671
	Choroid plexus epithelial cells	73	213	147	433
Glial cells	Oligodendrocyte progenitor cells	26	106	80	212
	Oligodendrocytes	88	114	208	410
	Schwann cells	74	119	137	330
	Microglia	52	337	220	609
Blood and immune cells	Macrophages & Monocytes	58	368	194	620
	Lymphocytes	204	213	174	591
Endothelial and mural cells	Vascular endothelial cells	120	206	235	561
	Pericytes	21	144	104	269
	Vascular smooth muscle cells	32	143	121	296
Mesenchymal cells	Fibroblasts	55	166	134	355

The cell types of the brain

The human brain contains an exceptionally diverse range of cell types, broadly divided into neuronal and non-neuronal cells. Neurons are the primary signaling units of the brain and can be classified based on their morphology, electrophysiological properties, neurotransmitter identity, and molecular expression profiles. A fundamental distinction is between excitatory and inhibitory neurons, primarily associated with glutamatergic and GABAergic neurotransmission, respectively. Other populations include specialized neurotransmitter neurons, such as dopaminergic, serotonergic, and cholinergic neurons, as well as neurosecretory neurons involved in hormonal regulation. Neurons can also be classified based on their connectivity, for example distinguishing between interneurons that primarily form local connections and projection neurons that transmit signals over longer distances. While interneurons are often inhibitory and projection neurons are typically excitatory, this is not a strict distinction, as both inhibitory projection neurons and excitatory interneurons exist.

Non-neuronal cells include endothelial cells lining blood vessels, ependymal cells lining the ventricles, and glial cells. Oligodendrocytes produce myelin that insulates neuronal axons, microglia serve as the resident immune cells of the brain, and astrocytes support numerous functions, including blood–brain barrier maintenance, tissue homeostasis, and neurotransmitter recycling.

Figure 1. Simplified schematic drawing of the main cell types of the brain, with the cell class color codes used in the resource.

Cell clusters in different brain regions

Expression profiles across cell clusters and brain regions are available for all protein-coding genes, searchable and clickable for more details. A bar chart of the cell types combined with regional details is shown in a bubble plot on each gene summary page. On the regional detail page the regional specific cells and expression is summarized.

GAD2 encodes glutamate decarboxylase 2, an enzyme involved in the synthesis of GABA, and is a well-established marker of inhibitory neurons. Its expression in the basal ganglia and thalamus highlights the distribution of GABAergic neuronal populations, including inhibitory projection neurons of the basal ganglia and the GABAergic neurons of the thalamus.

GAD2 - basal ganglia, neurons
GAD2 - thalamus, neurons

GAD2 - neuronal soma & synapses
ELAVL3 - neuronal soma
CBFA2T2 - neuronal nucleus
SLC17A7 - synapses

GFAP encodes glial fibrillary acidic protein, an intermediate filament protein and well-established marker of astrocytes. Single-nucleus RNA sequencing shows relatively uniform expression across the astrocyte cluster in the thalamus, whereas the cerebral cortex displays a clear expression gradient, highlighting regional differences and molecular heterogeneity among astrocyte populations.

GFAP - cerebral cortex, non-neuronal
GFAP - thalamus, non-neuronal

GFAP - astrocyte
MBP - oligodendrocyte
RGS10 - microglia
SPAG6 - ependymal cells

Background

Single nuclei RNAseq data

Siletti K et al. (2023) published single nuclei RNA sequencing result, based on over 3 million cells from multiple brain regions, in Science magazine and created an interactive portal (The Human Brain Cell Atlas v1.0 ) available for single cell exploration across human gene expression in healthy brain cells. The Human Protein Atlas aims to generate a comprehensive resource representing the human body and its complexity, and with a need for better representation of the different cell types of the human brain, we imported the expression profiles re-processed the data by reclustering, naming and grouping cell clusters into main cell types. This way providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). Some of the supercluster names were kept thanks to good correlation and overlap with the new cell cluster annotation. The expression profile of the different clusters is shown for each of the 11 different brain regions. More details, related to number of M reads and number of cells per brain region/UMAP can be found here. The published cerebral cortex data is represented by a larger number of cells, and we only included a random selection of 500 thousand cells. In total, expression data for 2526725 brain cells is displayed in the Brain single nuclei dataset, for browsing the gene expression and provide easy comparison to cell type expression in peripheral tissues.

3D imaging of the cells in the brain

By studying the cells in 3D, using light sheet microscopy and immunostaining it is possible to study the cells, their connections and processes in detail. This move briefly shows how the protein GPR151 is detected in neurons of the mouse thalamus with processes into other brain regions. The movie also includes detection of endothelial cells (PECAM1) and astrocytes (GFAP) in the mouse hippocampus. Extended version of the movie with more information about the orphan receptor GPR151 and the blood brain barrier is found here.