Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [DRG Spatial]

ABSTRACT: Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the mouse adult spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human DRG neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE243073 | GEO | 2024/01/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal snRNA-seq]

Project description:Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the mouse adult spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human DRG neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

2024-01-11 | GSE243076 | GEO

Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal spatial]

2024-01-11 | GSE243074 | GEO

Human motor neurons are rare in the spinal cord and can be transcriptomically divided into known subtypes divided into known subtypes.

Project description:Motor neurons are a rare neuronal subtype in the adult spinal cord. We performed single-nucleus RNA sequencing on nuclei extracted from adult human spinal cord and describe the transcriptional heterogeneity.

2023-04-06 | GSE228778 | GEO

Single-nucleus transcriptomic atlas of spinal cord neuron in human

Project description:Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and/or neural diseases, the underlying organization of neuronal clusters remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell and/or single-nucleus RNA-sequencing in various animal models. However, molecular evidence of neuronal heterogeneity in the human spinal cord has not yet been established. Here, we sought to classify spinal cord neurons from human donors using high-throughput single-nucleus RNA-sequencing. The functional heterogeneity among the identified cell types and signaling pathways that connect neuronal subtypes were explored. Moreover, we compared the transcriptional patterns obtained in human samples with previously published single-cell transcriptomic profiles of the mouse spinal cord. As a result, we generated the first comprehensive transcriptomic atlas of human spinal cord neurons and defined 18 neuronal clusters. In addition to identifying new and functionally distinct neuronal subtypes, our results also provide novel marker genes for previously described neuronal types. The comparison with mouse transcriptomic profiles revealed an overall similarity in the cellular composition of the spinal cord between the two species, while simultaneously highlighting some degree of heterogeneity. In summary, these results illustrate the complexity and diversity of neuronal types in the human spinal cord and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

2022-11-07 | GSE188255 | GEO

The neurons that restore walking after paralysis [snRNA-seq]

Project description:Here, we show that epidural electrical stimulation (EES) of the lumbar spinal cord applied during neurorehabilitation (EESREHAB) restored walking in nine people with chronic spinal cord injury (SCI). This recovery involved a reduction of the metabolic activity in the lumbar spinal cord during walking. We hypothesized that this unexpected reduction reflects activity-dependent selection of specific neuronal subpopulations that become essential to walk after SCI. To identify these putative neurons, we modelled the technological and therapeutic features underlying EESREHAB in mice. We applied single-nucleus RNA sequencing and spatial transcriptomics to the spinal cord of these mice to chart a spatially-resolved molecular atlas of recovery from paralysis. We then employed cell type and spatial prioritization to uncover the neurons involved in the recovery of walking. A single population of excitatory interneurons nested within intermediate laminae emerged. Although these neurons were not necessary to walk before SCI, we demonstrate that they are essential to regain walking following SCI. In turn, augmenting their activity instantly phenocopied the recovery of walking enabled by EESREHAB. We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after SCI. Moreover, our methodology establishes a framework to identify the neurons producing complex behaviours using molecular cartography.

2022-06-20 | GSE184370 | GEO

The neurons that restore walking after paralysis [spatial transcriptomics]

2022-06-20 | GSE184369 | GEO

Single-nucleus transcriptomic profiles of glial cells in human dorsal root ganglion and spinal cord

Project description:Glial cells are present throughout the entire nervous system and paly a crucial role in regulating physiological and pathological functions, such as infections, acute injuries and chronic neurodegenerative disorders. The glial cells mainly include astrocytes, microglia, and oligodendrocytes in the central nervous system (CNS), and satellite glial cells (SGCs) in the peripheral nervous system (PNS). Although the glial subtypes and functional heterogeneity is relatively well understood in mice by recent studies using single-cell or single-nucleus RNA-sequencing, no evidence yet has elucidate the transcriptomic profiles of glia cells in PNS and CNS. Here, we used high-throughput single-nucleus RNA-sequencing to map the cellular and functional heterogeneity of SGCs in human dorsal root ganglion (DRG), and astrocytes, microglia, and oligodendrocytes in human spinal cord. In addition, we compared the human findings with previous single-nucleus transcriptomic profiles of glial cells from mouse DRG and spinal cord. This work will comprehensively profile glial cells heterogeneity and will provide a powerful resource for probing the cellular basis of human physiological and pathological conditions related to glial cells.

2022-02-24 | GSE189501 | GEO

Spinal cord regeneration at single-cell resolution restores walking after paralysis

Project description:Although axon regeneration can now be induced experimentally across anatomically complete spinal cord injury (SCI), restoring meaningful function after such injuries has been elusive. This failure contrasts with the spontaneous, naturally occuring repair that restores walking after severe but incomplete SCI. Here, we applied projection-specific and comparative single-nucleus RNA sequencing to uncover the transcriptional phenotype and connectome of neuronal subpopulations involved in natural spinal cord repair. We identified a molecularly defined population of excitatory projection neurons in the thoracic spinal cord that extend axons to the lumbar spinal cord where walking execution centers reside. We show that regrowing axons from these specific neurons across anatomically complete SCI and guiding them to reconnect with their appropriate target region in the lumbar spinal cord restores walking in mice. These results demonstrate that mechanism-based repair strategies that recapitulate the natural topology of molecularly defined neuronal subpopulations can restore neurological functions. Expanding this principle to different classes of neurons across the central nervous system may unlock the framework to achieve complete repair of the injured spinal cord.

2023-09-20 | GSE198949 | GEO

Robust axonal regeneration occurs in the injured CAST/Ei mouse central nervous system

Project description:Axon regeneration in the central nervous system (CNS) requires reactivating injured neurons’ intrinsic growth state and enabling growth in an inhibitory environment. Using an inbred mouse neuronal phenotypic screen, we find that CAST/Ei mouse adult dorsal root ganglion neurons extend axons more on CNS myelin than the other eight strains tested, especially when pre-injured. Injury-primed CAST/Ei neurons also regenerate markedly in the spinal cord and optic nerve more than those from C57BL/6 mice and show greater spouting following ischemic stroke. Heritability estimates indicate that extended growth in CAST/Ei neurons on myelin is genetically determined, and two whole-genome expression screens yield the Activin transcript Inhba as most correlated with this ability. These screens are presented here. Biological quadruplicate - Mouse tissue - Naïve Dorsal Root Ganglia (DRG) and 5 day post sciatic nerve crush DRG - x9 strains.

2015-07-22 | E-GEOD-67130 | biostudies-arrayexpress

Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons

Project description:To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse.

2020-12-31 | GSE161621 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data