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The neuronal cell-specific proteomeThe function of the brain, defined as the central nervous system, is to receive, process and execute the coordinated higher functions of perception, motion and cognition that signify human life. The cellular components of the underlying and highly complex network of transmitted signals include neurons and supportive glial cells. Transcriptome analysis shows that 78% (n=15733) of all human proteins (n=20162) are detected in neuronal cells and 1782 of these genes show an elevated expression in any neuronal cells compared to other brain cell types. The neuronal cells are represented by 21 different clusters, the data and the naming is based on Siletti K et al. (2023), where the cluster names are a combination of regional representation and literature. Note: the neuronal cluster names are not the same as cell types, but rather a collected name for that cluster of neurons, which may include several different neuronal subtypes, and some neuronal subtypes can be found in several neuronal clusters. The neuronal clusters vary across the 11 different brain regions. The 21 neuronal superclusters are named amygdala excitatory, cerebellar inhibitory, CGE interneuron, deep-layer corticothalamic and 6b, deep-layer intratelencephalic, deep-layer near-projecting, eccentric medium spiny neuron, hippocampal CA1-3, hippocampal CA4, hippocampal dentate gyrus, LAMP5-LHX6 and Chandelier, lower rhombic lip, mammillary body, medium spiny neuron, MGE interneuron, midbrain-derived inhibitory, miscellaneous, splatter, thalamic excitatory, upper rhombic lip, upper-layer intratelencephalic. The vesicular glutamate transporter (VGLUT2, also called SLC17A6), mainly expressed by glutamatergic neurons in subcortical regions, is detected in several of the neuronal clusters, highest expression is observed in the thalamic interneuronal cluster and lower rhombic lip cluster, and the gene is classified as group enriched. On protein level, detected by immunolabeling, we can observe a synaptic location, especially in the synaptic glomeruli of cerebellar granular layer, and along the dendritic arbour of the Purkinje cells. Choline acetyltransferase (CHAT) is expressed by cholinergic neurons, sparesly detected, in selected clusters and brain regions. On protein level, we can observe CHAT in a subset of large neurons in caudate nucleus (basal ganglia). The neuronal cell transcriptomeThe snRNA-seq-based neuronal cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in neuronal cell type compared to other brain cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
Table 1. Number of genes in the subdivided specificity categories of elevated expression in the analyzed neuronal cell types.
General neuronal markersNeuronal cells are highly variable, for example with regard to the signaling properties, what neurotransmitter they use as a pre-synaptic neuron, as well as the receptors and ability to receive different types of input as a post-synaptic neuron. Additionally, the regional variation and circuitry (connectivity) plays a role in the identity of a neuron. However, certain markers are pan-neuronal, such as RBFOX3, also called NeuN, which was utilized for neuronal enrichment when generating the data, by Siletti K et al. (2023).
Inhibitory vs excitatory neuronsInterneurons, which typically have local connections, are often inhibitory, meaning they reduce the membrane potential and decrease the likelihood of action potential propagation in the postsynaptic neuron. Common neurotransmitters released by inhibitory neurons include GABA and glycine. As a result, proteins associated with these molecules, such as GAD1 and GAD2—both essential for GABA synthesis—are often used as markers for inhibitory neurons. In contrast, long-range projecting neurons are usually excitatory, increasing the membrane potential in the postsynaptic neuron. Glutamate is a common excitatory neurotransmitter, and markers for these neurons include various glutamate transporters like VGLUT1 and VGLUT2, also known as SLC17A7 and SLC17A6. The separation of inhibitory and excitatory neurons is observed when comparing the cluster expression overview.
Amygdala excitatoryAlthough the name of this cluster is amygdala excitatory, cells of this cluster is not limited to the amygdala. The amygdala excitatory cluster of cells are found in forebrain and midbrain regions, while missing from the hindbrain regions. As shown in Table 1, 39 genes show elevated expression in amygdala excitatory compared to other brain cell clusters. Among the genes classified as elevated in the amygdala excitatory cluster there are variation across the different brain regions and overlap with other clusters. OTP, ARHGAP36 and C22orf42, all show highest expression in the thalamus in the amygdala excitatory cluster, and is combined with high expression in the splatter cluster. C22orf42 is expressed by the Amygdala excitatory cluster and splatter cluster, and show expression in the thalamic excitatory cluster, mainly in the basal ganglia. In contrast, SLC22A10, SLC30A3 and SLC22A9 are all transporters with an elevated expression level in the amygdala excitatory cluster, across all represented brain regions, and they are all combined with high expression levels in the upper-layer intratelencephalic cluster. In the case of TRIM54, the amygdala excitatory cluster, with intratelencephalic cluster cells are accompanied by the hippocampal dentate gyrus cluster. In contrast, the genes with high expression in the amygdala excitatory cluster cells found in the midbrain shows an overlap with a variety of clusters, MS4A8 show high expression in upper-layer intratelencephalic cluster cells and also choroid plexus epithelial cells, MEPE show high expression in MGE interneurons and TG show high expression in hippocampal CA4 cluster cells as well as some glial and vasculature cells. Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The amygdala excitatory can be explored to further investigate subtypes of cells across the different brain regions.
Cerebellar inhibitoryThe cerebellar inhibitory cluster is at the top regarding number of genes classified as enriched. As shown in Table 1, 177 genes show elevated expression in Cerebellar inhibitory compared to other brain cell clusters. Secretagogin (SCGN) is a secreted calcium-binding protein and often used as a marker for interneurons of the molecular layer of cerebellum, secretagogin also has an important role in the pancreatic islet cells.
Several of the genes with elevated expression in cerebellar inhibitory neurons are also highly expressed in retinal neurons. Retina is not included in this specific dataset, but we can easily compare the datasets on the gene summary page, across the datasets. BSPH1 expressed by bipolar cells, CPLX4 expressed by photoreceptor cells and bipolar cells, and BHLHE22 horizontal cells and bipolar cells, are all showing elevated expression in the cerebellar inhibitory cluster. TFAP2B is a transcription factor with highest expression in retinal horizontal cells, comparing cell types across the body, also has the highest expression level in the cerebellar inhibitory cells of the brain. The protein detection is possible using IHC and imaging pipeline of the Tissue Atlas, showing the nuclear protein location in retina as well as the molecular layer of cerebellar cortex.
By investigating markers for different inhibitory neurons, the cerebellar inhibitory cluster mainly includes the molecular layer neurons, stellate and basket cells. BHLHE22 and TFAP2B (mentioned above) are both markers for molecular layer interneurons of the cerebellar cortex. While, the Purkinje cells is part of the miscellaneous cluster, based on a comparison of the Purkinje cell specific PCP4 gene expression and HOMER3, which is expressed in both the miscellaneous and cerebral inhibitory, and on protein level detected in both Purkinje cells and interneurons of the molecular layer. KIT, KIT proto-oncogene, receptor tyrosine kinase, provides an interesting case since it is expressed in the cerebellar inhibitory cluster as well as the midbrain-derived inhibitory cluster. Suggesting KIT is expressed in more cells than basket cells, while on protein level KIT is detected at the Pinceau synapse of the Purkinje cell's axon initial segment, which is in literature suggested to be related to basket cells. Exploring the cerebellar inhibitory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The cerebellar inhibitory can be explored to further investigate subtypes of cells across the different brain regions.
CGE interneuronCaudal ganglionic eminences (CGE) is a subcortical structure, and the origin of several subtypes of interneurons. One difference between the CGE and MGE derived interneurons is that CGE rarely express PVALB, and this is a difference observed in the PVALB expression profile. As shown in Table 1, 105 genes show elevated expression in the CGE interneuron cluster compared to other brain cell clusters. Among the genes with elevated expression we can find Vasoactive intestinal peptide, VIP, highly expressed and specific for the CGE interneuron cluster. VIP can act as neurotransmitter and neuromodulator, it is a key marker to separate different types of cortical interneurons. The ligand-gated ion channel and serotonin transporter HTR3A is also classified as enriched among CGE interneurons compared to other cell clusters in the brain. The cells with overlapping expression of VIP and HTR3A could be bipolar cells, a cortical interneuronal subtype, based on suggested dependency of serotonergic inputs (Wong FK et al. (2022)). Cholecystokinin CCK, often mentioned in interneuronal subclassification, is also found among the genes with elevated expression in the CGE interneuron cluster. Calretinin (CALB2), a calcium-binding protein expressed by subtypes of neurons, especially interneurons in cerebral cortex and hippocampus, show elevated expression in the CGE interneuron cluster, as well as the lower rhombic lip cluster and thalamic excitatory cluster cells (not in cerebral cortex).
Exploring the CGE interneuron clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The CGE interneurons can be explored to further investigate subtypes of cells across the different brain regions.
Deep-layer corticothalamic and 6bAs shown in Table 1, 84 genes show elevated expression in Deep-layer corticothalamic neurons and 6b, compared to other brain cell clusters. The 4 genes with enriched expression profile in this cluster are all rather low abundant and when examining the cluster variation, heterogenous and only detected in a smaller subsets of the cells within the cluster. Otolin 1 (OTOL1) is evenly expressed across the brain regions, Lymphocyte antigen 6 family member D (LY6D) is mainly found in the thalamic sample while Keratin 17 (KRT17) show more expression in Basal ganglia and Midbrain samples. Among the group enriched genes, we can find SATB2 a transcription factor and marker for excitatory projecting neurons.
Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Deep-layer corticothalamic and 6b can be explored to further investigate subtypes of cells across the different brain regions.
Deep-layer intratelencephalicAs shown in Table 1, 57 genes show elevated expression in Deep-layer intratelencephalic neurons compared to other brain cell clusters. SATB2 a transcription factor and marker for excitatory projecting neurons, is classified as group enriched and shared with other cell clusters, such as deep-layer corticothalamic and 6b. The dopamine receptor D5 (DRD5) show high expression in this cluster of neurons. The two genes classified as enriched in this cluster cell type are SMYD1 and UCMA, both with highest expressionin the Amygdala, and the later almost selectively expressed in the Amygdala. These genes are expressed by different cells of this cluster, noted by comparing the UMAP expression overview. Among the group enriched or enhanced expression profiles there are several genes shared with the cluster upper-layer intratelencephalic, for examples MCHR2 and KCNV1. Also, shared genes with the deep-layer corticothalamic and 6b cluster, as in the case of SLC22A9. While genes such as CPNE4 and SLC30A3 share the elevated expression with the Hippocampal CA4 cluster. Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The deep-layer intratelencephalic can be explored to further investigate subtypes of cells across the different brain regions.
Deep-layer near-projectingThe deep-layer near-projecting cluster includes neurons detected in the forebrain regions. As shown in Table 1, 127 genes show elevated expression in Deep-layer near-projecting neurons compared to other brain cell clusters. GNAT3 is an example of a gene with enriched expression in the deep-layer near-projecting cluster and is also detected by immunohistochemistry in a subset of neurons.
Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Deep-layer near-projecting cluster can be explored to further investigate subtypes of cells across the different brain regions.
Eccentric medium spiny neuronThe Eccentric medium spiny neurons include cells detected in the forebrain regions. This cluster is especially prominent in amygdala, basal ganglia and hypothalamus. As shown in Table 1, 114 genes show elevated expression in Eccentric medium spiny neuron compared to other brain cell clusters. Neurons of this cluster are inhibitory neurons, expressing both GAD1 and GAD2, where GAD2 is classified as group enriched in this cluster along with other interneuronal containing cell clusters. The Dopamine receptor D1 (DRD1)show enriched expression in this cluster, and Tyrosine hydroxylase (TH) show elevated expression. Exploring the Eccentric medium spiny neuron clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Eccentric medium spiny neuron can be explored to further investigate subtypes of cells across the different brain regions.
Hippocampal CA1-3The hippocampal CA1-3 cluster is only represented in cerebral cortex, amygdala and hippocampus. As shown in Table 1, 80 genes show elevated expression in Hippocampal CA1-3 neurons compared to other brain cell clusters. The 2 genes with enriched expression, are both related to cerebral cortex, while genes like CLPSL1 are more evenly expressed in this cluster when comparing the regional variation. Among the genes with elevated expression in the Hippocampal CA1-3 cluster, TAC1 is detected, which show selective protein location to large neurons in the cerebral cortex.
Exploring the hippocampal CA1-3 clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The hippocampal CA1-3 can be explored to further investigate subtypes of cells across the different brain regions.
Hippocampal CA4As shown in Table 1, 143 genes show elevated expression in Hippocampal CA4 neurons compared to other brain cell clusters. Out of the 3 genes classified as cell type enriched for the cluster, both BHMT and KREMEN2 are highly expressed in the Hippocampal CA4 cluster related to the midbrain region, while MYPN show high expression in the Hippocampal CA4 cluster in both midbrain and hippocampus. The Neurogenic differentiation factor 6 (NEUROD6) show highest expression in the Hippocampal CA4 cluster of cells.
Exploring the Hippocampal CA4 clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The hippocampal CA4 cluster can be explored to further investigate subtypes of cells across the different brain regions.
Hippocampal dentate gyrusAs shown in Table 1, 163 genes show elevated expression in Hippocampal dentate gyrus neurons compared to other brain cell clusters. The Hippocampal dendate gyrus cluster of cells show variation across the brain regions. Among the genes with enriched expression profile, only THOC3 show a general high expression in this cluster in the three brain regions represented. TNNT2 and CHRNA1 show high expression in hippocampus and thalamus, while ADGRG4 mainly show expression in the midbrain cluster, and SCART1 show highest expression in hippocampus and AQP9 in the thalamus cluster. Exploring the hippocampal dentate gyrus clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The hippocampal dentate gyrus can be explored to further investigate subtypes of cells across the different brain regions.
LAMP5-LHX6 and ChandelierThe LAMP5-LHX6 and Chandelier cluster cells are present in forebrain regions and midbrain. The name of this cluster is based on a defined cell group expressing LAMP5 and LHX6, both genes with highest expression in this cluster. As shown in Table 1, 127 genes show elevated expression in LAMP5-LHX6 and Chandelier cells compared to other brain cell clusters. This cluster includes inhibitory neurons, resulting in elevated expression of GAD2. Dopamine receptor D5 (DRD5) show elevated expression in this cluster, as well as Carbonic anhydrase 1(CA1), and 3 (CA3). Both carbonic anhydrase, as well as several other genes, such as ZPBP, aNXPH1 and FBN2 show an overlap between expression in this cluster and oligodendrocyte lineage cells.
Exploring the LAMP5-LHX6 and Chandelier clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The LAMP5-LHX6 and Chandelier can be explored to further investigate subtypes of cells across the different brain regions.
Lower rhombic lipThe Lower rhombic lip cluster is only represented in basal ganglia, midbrain, pons and medulla oblongata. As shown in Table 1, 198 genes show elevated expression in Lower rhombic lip neurons compared to other brain cell clusters. Neurofilament light (NEFL), medium (NEFM) and heavy (NEFH) chain, all show elevated expression levels in this cluster. Tubulointerstitial nephritis antigen (TINAG) is a basement membrane glycoprotein with selective expression in this cluster. BarH like homeobox 1 (BARHL1) is an example of a gene with shared enriched expression in the lower and upper rhombic lip clusters. Calretinin (CALB2), a calcium-binding protein expressed by subtypes of neurons, especially interneurons in cerebral cortex and hippocampus, show elevated expression in the CGE interneuron cluster as well as the lower rhombic lip cluster and thalamic excitatory cluster cells.
Exploring the Lower rhombic lip clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Lower rhombic lip can be explored to further investigate subtypes of cells across the different brain regions.
Mammillary bodyThe Mammillary body cluster is only represented in the hypothalamus. Anatomically the mammillary bodies are round small parts of the posterior hypothalamic region. As shown in Table 1, 146 genes show elevated expression in Mammillary body neurons compared to other brain cell clusters. Some examples of genes with elevated expression in this cluster are: internexin neuronal intermediate filament protein alpha (INA), which is detected in all cluster types, but with elevated expression in this cluster. The transcription factor LIM homeobox 1 (LHX1) show highest expression in this cluster. Two serotonin receptors with variable expression across the neuronal cell population, 5-hydroxytryptamine receptor 7 (HTR7), and 2A (HTR2A) also show highest expression in this cluster. Thyrotropin releasing hormone (TRH) is highly expressed in this cluster. Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Mammillary body can be explored to further investigate subtypes of cells across the different brain regions.
Medium spiny neuronThe Medium spiny neuron cluster is present in forebrain regions. Medium spiny neuron is the name of inhibitory neurons of the basal ganglia. As shown in Table 1, 194 genes show elevated expression in Medium spiny neuron compared to other brain cell clusters. Dopamine receptor D2 (DRD2) is classified as cell type enriched in this cluster, and known marker for the medium spiny neurons of the basal ganglia, as well as DRD2, which is classified as group enriched in this cluster. A serotonin receptor with variable expression across the neuronal cell population, 5-hydroxytryptamine receptor 4 (HTR4) show highest expression in this cluster, and so does calbindin 1 CALB1. Calbindin is a calcium-binding protein often used for sub-clustering neuronal cell types, and is detected in a subset of neurons in cerebral cortex using immunohistochemistry.
Exploring the medium spiny neuron clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The medium spiny neuron can be explored to further investigate subtypes of cells across the different brain regions.
MGE interneuronthe MGE interneuron cluster is present in forebrain regions and midbrain, and it shows expression overlap with CGE interneuron cluster. As shown in Table 1, 90 genes show elevated expression in MGE interneuron compared to other brain cell clusters. The neuronal marker, ELAV like RNA binding protein 2 (ELAVL2) show highest expression in this cluster. Several genes with elevated expression are shared with the CGE interneuron cluster, for example DLX1 and TAC3. Somatostatin (SST) is a well-studied peptide hormone, expressed by both MGE interneurons and the splatter cluster.
Exploring the MGE interneuron clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The MGE interneuron can be explored to further investigate subtypes of cells across the different brain regions.
Midbrain-derived inhibitoryThe Midbrain-derived inhibitory cluster is not represented in cerebral cortex, hippocampus and spinal cord. And the largest representation with big clear clusters are found in the midbrain, thalamus, hypothalamus and pons. As shown in Table 1, 167 genes show elevated expression in Midbrain-derived inhibitory neurons compared to other brain cell clusters. This cluster of neurons has several genes classified as enriched, indicating a distinct expression profile compared to other neurons. Prolactin (PRL) is highly enriched in this cluster, and so is the transcription factor SOX14. Additionally, a serotonin receptors with variable expression across the neuronal cell population, 5-hydroxytryptamine receptor 2A (HTR2A) show high expression in this cluster. Glutamate receptor interacting protein 2 (GRIP2) and Glutamate ionotropic receptor kainate type subunit 1 (GRIK1) both show highest expression in this cluster. Exploring the midbrain-derived inhibitory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The midbrain-derived inhibitory can be explored to further investigate subtypes of cells across the different brain regions.
MiscellaneousDue to the complexity of the brain, and numerous subtypes of neurons, the miscellaneous cluster includes several distinct cell clusters and varies across the different brain regions. In the original data, the miscellaneous cluster also includes leukocytes. However, since they were assigned a cell type, we separated them from the neurons of this cluster, making miscellaneous a purely neuron cluster to compare with the other neuronal clusters of the brain. This cluster is represented in the forebrain regions and midbrain. As shown in Table 1, 36 genes show elevated expression in Miscellaneous neurons compared to other brain cell clusters. The Neurogenic differentiation factor 6 (NEUROD6) show elevated expression in this cluster, as well as SATB2, a transcription factor and marker for excitatory projecting neurons. While some genes with elevated expression are detected throughout all represented regions, such as GRB14 and KCNB2, others show regional variation, like PTTG1 and RSPO2 both with a higher expression in thalamus and midbrain, while SLC26A4 is lacking expression in thalamus and midbrain. FST show elevated in the Amygdala represented miscellaneous Exploring the amygdala excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The miscellaneous cluster can be explored to further investigate subtypes of cells across the different brain regions.
SplatterThe Splatter cluster includes a mix of neuronal cell types across all regions, this is also the reason behind the supercluster name, as explained by Siletti K et al. (2023). When separating the superclusters into the 11 brain regions the cells assigned to the splatter cluster are often closely clustering some other cluster. In cerebral cortex the splatter cluster are partly integrated with the MGE interneuronal cluster, and this seems to be the case for all forebrain regions - the splatter cluster is part of interneuronal cell clusters. However, for midbrain and hindbrain regions, the splatter cluster seems more heterogenous and complex. As shown in Table 1, 97 genes show elevated expression in Splatter neurons compared to other brain cell clusters. And as mentioned, the cell identity of this cluster is heterogenous, with a forebrain vs other brain regions trend. Neuropeptide Y (NPY) expressing neurons are found in the splatter cluster in cerebral cortex and amygdala.
In the hypothalamus cell data, the splatter cluster includes potential magnocellular neurosecretory cells, based on the expression of oxytocin (OXT) and vasopressin (AVP). Exploring the splatter clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The splatter can be explored to further investigate subtypes of cells across the different brain regions.
Thalamic excitatoryThe Thalamic excitatory cluster is not limited to thalamic neurons, however, thalamus has the largest representation of this cluster, while lower numbers of neurons assigned to this cluster are present in cerebral cortex, basal ganglia and midbrain. As shown in Table 1, 124 genes show elevated expression in Thalamic excitatory neurons compared to other brain cell clusters. The transcription factor gastrulation brain homeobox 2 GBX2 show shared expression between thalamic excitatory cluster cells and glial cells. This cluster includes excitatory neurons, and high expression levels of the glutamate transporters VGLUT2 (SLC17A6), with immunohistochemistry VGLUT2 show a synaptic location.
Exploring the thalamic excitatory clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The thalamic excitatory can be explored to further investigate subtypes of cells across the different brain regions.
Upper rhombic lipThe Upper rhombic lip cluster is represented in most regions, except hippocampus and amygdala. And the cluster, in regard to cell number and clear clustering, is prominent in midbrain and hindbrain regions. As shown in Table 1, 249 genes show elevated expression in Upper rhombic lip neurons compared to other brain cell clusters. BarH like homeobox 1 (BARHL1) is an example of a gene with shared enriched expression in the lower and upper rhombic lip clusters. EOMES is a transcription factor, that plays an important role in neurodevelopment Lv X et al. (2019), with enriched expression in this cluster, combined with leukocytes. Glutamate metabotropic receptor 4 (GRM4) and transcription factor UNC homeobox (UNCX) are more examples of genes with elevated expression in this cluster. While, EN2 and CRTAM both are examples of enriched genes shared between this cluster and cerebellar interneurons. Exploring the upper rhombic lip clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The upper rhombic lip can be explored to further investigate subtypes of cells across the different brain regions.
Upper-layer intratelencephalicThe Upper-layer intratelencephalic cluster of neurons are found in the forebrain and midbrain regions of the brain. As shown in Table 1, 81 genes show elevated expression in Upper-layer intratelencephalic neurons compared to other brain cell clusters. Among the genes with elevated expression in this cluster there are several solute carriers, such as SLC22A10, SLC22A24 and SLC22A25 all with highest expression in this cluster, as well as SLC22A6, SLC22A9 and SLC30A3 with group enriched or enhanced expression levels. In addition, this cluster includes several potassium voltage-gated channel- related proteins with elevated expression profile, such as KCNV1, KCNH1, KCNS1 and KCNH4. Exploring the upper-layer intratelencephalic clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The upper-layer intratelencephalic can be explored to further investigate subtypes of cells across the different brain regions. BackgroundSingle nuclei RNAseq dataSiletti 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 and grouped them based on our cell type- strategy (providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). We based the cell type clusters on the 31 superclusters, as well as the provided assigned cell types, and the data is shown as 34 different "supercluster cell types". 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 resource, for browsing the gene expression and provides easy comparison to cell type expression in peripheral tissues. Relevant publications Uhlén M et al., Tissue-based map of the human proteome. Science (2015) |
The Human Protein Atlas project is funded
