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

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

PROVIDER: PRJNA1016331 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26050447.fastq.gz	Fastqsanger.gz
	SRR26050448_1.fastq.gz	Fastqsanger.gz
	SRR26050448_2.fastq.gz	Fastqsanger.gz
	SRR26050449_1.fastq.gz	Fastqsanger.gz
	SRR26050449_2.fastq.gz	Fastqsanger.gz

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

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 | GSE243073 | GEO

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

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

2024-01-11 | GSE243076 | GEO

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

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

| PRJNA1016330 | ENA

A harmonized atlas of spinal cord cell types and their computational classification

Project description:Single cell sequencing is transforming many fields of science but the vast amount of data it creates has the potential to both illuminate and obscure underlying biology. To harness the exciting potential of single cell data for the study of the mouse spinal cord, we have created a harmonized atlas of spinal cord transcriptomic cell types that unifies six independent and disparate studies into one common analysis. With the power of this large and diverse dataset, we reveal spinal cord cell type organization, validate a combinatorial set of markers for in-tissue spatial gene expression analysis, and optimize the computational classification of spinal cord cell types based on transcriptomic data. This work provides a comprehensive resource with unprecedented resolution of spinal cord cell types and charts a path forward for how to utilize transcriptomic data to expand our knowledge of spinal cord biology.

2020-12-31 | GSE158380 | GEO

Spatial transcriptomics on human lumbar spinal cord

Project description:This study includes spatial transcriptomics on the human lumbar spinal cord using the 10x Genomics Visium platform. Frozen sections of spinal cord were placed on Visium slide arrays and processed using the 10x Genomics workflow, followed by alignment and quantification using the spaceranger package.

2023-01-31 | GSE222322 | GEO

Spatial transcriptomics on human lumbar spinal cord

Project description:Spatial transcriptomics on human lumbar spinal cord

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RNA-Seq of DRG and dorsal cord after nerve injury

Project description:Genes are up and down regualted in DRG and spinal dorsal cord after peripheral nerve injury WT male adult with sciatic and femoral nerve transection 7 days, RNA was purified from ipilateral or contralateral L4-L6 DRGs or lumbar spinal dorsal cords

2015-12-10 | E-GEOD-66619 | biostudies-arrayexpress

RNA-Seq of DRG and dorsal cord after nerve injury

Project description:Genes are up and down regualted in DRG and spinal dorsal cord after peripheral nerve injury

2015-12-10 | GSE66619 | GEO

Spatiotemporal multi-omics decoding of the developing human spinal cord II

Project description:The human spinal cord contains diverse cell types, governed by a series of spatiotemporal events for tissue assembly and functions. However, the regulation of cell fate specification in the human developing spinal cord remains largely unknown. By performing single-cell and spatial multi-omics methods, we integrated the datasets and created a comprehensive human developmental atlas of the first trimester spinal cord. Unexpectedly, we discovered unique events in human spinal cord development, including early loss of active neural stem cells, simultaneous occurrence of neurogenesis and gliogenesis, and distinct spatiotemporal genetic regulations of fate choices. We also identified distinct regulations of cancer stem cells in ependymomas from our atlas. Thus, we demonstrate spatiotemporal genetic regulation of human spinal cord development and its potential to understand novel disease mechanisms.

2023-04-25 | GSE219121 | GEO

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