Comprehensive identification and spatial mapping of habenular neuronal types using single cell RNAseq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA414719 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: Not available
| S-EPMC6042852 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-03-23 | GSE105115 | GEO
Project description:The lateral habenula (LHb) is an epithalamic brain structure critical for processing and adapting to negative action outcomes. However, despite the importance of LHb to behavior and the clear anatomical and molecular diversity of LHb neurons, the neuron types of the habenula remain unknown. Here, we use high-throughput single-cell transcriptional profiling, monosynaptic retrograde tracing, and multiplexed FISH to characterize the cells of the mouse habenula. We find five subtypes of neurons in the medial habenula (MHb) that are organized into anatomical subregions. In the LHb, we describe four neuronal subtypes and show that they differentially target dopaminergic and GABAergic cells in the ventral tegmental area (VTA). These data provide a valuable resource for future study of habenular function and dysfunction and demonstrate neuronal subtype specificity in the LHb-VTA circuit.
2020-03-15 | GSE146983 | GEO
Project description:Molecular profiling of physiologically-defined neuronal types
| PRJNA524318 | ENA
Project description:The mammalian brain consists of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled (~4.0 million cells passing quality control), and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into four nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present a newly developed online platform, Allen Brain Cell (ABC) Atlas, to visualize the mouse whole brain cell type taxonomy and atlas along with the scRNA-seq and MERFISH data and metadata sets. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate myriad modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cellular and circuit function, development, and evolution of the mammalian brain.
2023-11-14 | GSE246717 | GEO
Project description:Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks
| PRJNA799264 | ENA
Project description:The medulla is the largest neuropil of the Drosophila optic lobe. It contains about 100 neuronal types that have been comprehensively characterized morphologically and molecularly. These neuronal types are specified from a larval neuroepithelium called the Outer Proliferation Center (OPC) via the integration of temporal, spatial, and Notch-driven mechanisms. Although we recently characterized the temporal windows of origin of all medulla neurons, as well as their Notch status, their spatial origins remained unknown. Here, we isolated cells from different OPC spatial domains and performed single-cell mRNA-sequencing to identify the neuronal types produced in these domains. This allowed us to characterize in a high-throughput manner the spatial origins of all medulla neurons.
2024-02-05 | GSE254562 | GEO
Project description:Using microarray, we compared the transcriptome of the wild-type and Gbx2-KO thalamus at E12.5. We show that Gbx2 promotes thalamic but inhibits habenular molecular characters.
2015-12-01 | GSE71690 | GEO
Project description:Neurons utilize glucose to generate adenosine triphosphate (ATP) essential for their survival, excitability and synaptic signaling, as well as initiating changes in neuronal structure and function. Defects in oxidative metabolism and mitochondria functions are also associated with aging and diverse human neurological diseases1-4. While neurons are known to adapt their metabolism to meet the increased energy demands of complex behaviors such as learning and memory, the molecular underpinnings regulating this process remain poorly understood4-6. Here we show that the orphan nuclear receptor estrogen related receptor gamma (ERRĪ³) becomes highly expressed during retinoic-acid induced neurogenesis and is widely expressed in neuronal nuclei throughout the brain. Mechanistically, we show that ERRĪ³ directly orchestrates the expression of networks of genes involved in mitochondrial oxidative phosphorylation and energy generation in neurons. The importance of this regulation is evidenced by decreased adaptive metabolic capacity in cultured neurons lacking ERRĪ³, and reduced long-term potentiation (LTP) in ERRĪ³-/- hippocampal slices. Notably, the defect in LTP was rescued by the metabolic intermediate pyruvate, functionally linking the ERRĪ³ knockout metabolic phenotype and memory formation. Consistent with this notion, mice lacking neuronal ERRĪ³ exhibit defects in spatial learning and memory. These findings implicate ERRĪ³ in the metabolic adaptations required for long-term memory formation. We used microarray analysis to compare the genome-wide gene expression changes between wild type (WT) and ERRĪ³-/- P0 cerebral cortex as it contains mainly neuronal lineage at this stage compared to adult cortex.
2015-09-03 | E-GEOD-47133 | biostudies-arrayexpress
Project description:The generation of specific types of neurons from stem cells offers important opportunities in regenerative medicine. However, future applications and proper verification of cell identities will require stringent ways to generate homogenous neuronal cultures. Here we show that under permissive culturing conditions individual transcription factors can induce a desired neuronal lineage from virtually all expressing cells by a mechanism resembling developmental binary cell fate switching. Such efficient selection of cell fate resulted in remarkable cellular enrichment that enabled global gene expression validation of generated neurons and identification of novel features in the studied cell lineages. Several sources of stem cells have a limited competence to differentiate into e.g. dopamine neurons. However, we show that the combination of factors that normally promote either regional or dedicated neuronal specification can overcome limitations in cellular competence and promote efficient reprogramming also in more remote neural contexts, including human neural progenitor cells. We used microarray analysis to verify the identity of several mESC derived neuronal cell types. By genome-wide gene expression comparisons we gained novel insights into molecular properties of several clinical relevant neuronal cell types. Total RNA was extracted from wild-type and transcription-factor induced mESC derived post-mitotic neurons and hybridized on Affymetrix arrays. In total triplicates of 9 different samples were analyzed. Wild-type samples served as control samples.
2011-03-04 | E-GEOD-27655 | biostudies-arrayexpress