Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Neuronal cell lines as model dorsal root ganglion neurons: a transcriptomic comparison

ABSTRACT: Aim: Dorsal root ganglion neuron-derived immortal cell lines including ND7/23 and F-11 cells have been used extensively as in vitro model systems of native peripheral sensory neurons. However, while it is clear that some sensory neuron-specific receptors and ion channels are present in these cell lines, a systematic comparison of the molecular targets expressed by these cell lines with intact peripheral neurons is lacking. Methods: we examined the expression of RNA transcripts in the human neuroblastoma-derived cell line, SH-SY5Y, and two dorsal root ganglion hybridoma cell lines, F-11 and ND7/23, using Illumina next-generation sequencing. Results: The expression profile of these three cell lines did not resemble any specific dorsal root ganglion neuron subclass. The cell lines lacked many markers for nociceptive sensory neurons, such as the transient receptor potential V1 gene, but expressed markers for both myelinated and unmyelinated neurons. Conclusion: This paper provides insights into the receptor repertoire expressed in common dorsal root ganglion neuron-derived cell lines, and illustrates the limits and potentials of these cell lines as tools for neuropharmacological exploration.

OTHER RELATED OMICS DATASETS IN: PRJNA305060PRJNA305415

ORGANISM(S): Mus musculus Rattus rattus Homo sapiens

PROVIDER: GSE75811 | GEO | 2016/05/01

SECONDARY ACCESSION(S): PRJNA305415

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [Wafergen]

Project description:Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.

2021-01-27 | GSE165566 | GEO

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [SmartSeq2]

2021-01-27 | GSE165553 | GEO

RNA-Seq of single cells from the mouse lumbar dorsal root ganglion

Project description:In order to establish a consensus catalog of dorsal rott ganglion cell types, we used comprehensive transcriptome analysis of single cells for unsupervised identification and molecular classification of sensory neurons independent of any a priori knowledge of sensory subtypes. RNA-Seq was performed on 799 dissociated single cells dissected from the mouse lumbar dorsal root ganglion distributed over a total of nine 96-well plates

2014-11-24 | E-GEOD-59739 | biostudies-arrayexpress

Ribotag analysis of proprioceptive dorsal root ganglion neurons in cell culture

Project description:We analyzed ribosome-associated RNA (raRNA) in dorsal root ganglion neurons in TrkC+ proprioceptive dorsal root ganglion neurons in cell culture.

2018-04-25 | GSE110374 | GEO

Scaling proprioceptor gene transcription by retrograde NT3 signaling

Project description:Transcriptional analysis of identified DRG subpopulations. Cell-type specific intrinsic programs instruct neuronal subpopulations before target-derived factors influence later neuronal maturation. Retrograde neurotrophin signaling controls neuronal survival and maturation of dorsal root ganglion (DRG) sensory neurons, but how these potent signaling pathways intersect with transcriptional programs established at earlier developmental stages remains poorly understood. Here we determine the consequences of genetic alternation of NT3 signaling on genome-wide transcription programs in proprioceptors, an important sensory neuron subpopulation involved in motor reflex behavior. We find that the expression of many proprioceptor-enriched genes is dramatically altered by genetic NT3 elimination, independent of survival-related activities. Combinatorial analysis of gene expression profiles with proprioceptors isolated from mice expressing surplus muscular NT3 identifies an anticorrelated gene set with transcriptional levels scaled in opposite directions. Voluntary running experiments in adult mice further demonstrate the maintenance of transcriptional adjustability of genes expressed by DRG neurons, pointing to life-long gene expression plasticity in sensory neurons. We combined a mouse line expressing GFP under the control of the TrkC promoter (BAC transgene approach) with various NT3 signaling mutants in order to identify the transcriptional changes in identified subpopulations of dorsal root ganglia (DRG) neurons. Sorted cells were processed for RNA extraction and hybridization on Affymetrix microarrays. Analysis was performed a postnatal (p) day p0. Subsequent analysis focused on the transcriptional profile of DRG neuron subpopulations at specific lumbar levels. Additional work addressed the transcriptional changes in whole DRG in adult mice with and without physical exercise.

2012-08-23 | E-GEOD-38074 | biostudies-arrayexpress

Whole transcriptome analysis of FACS purified somatosensory neuron subtypes and whole dorsal root ganglia tissue

Project description:The goal of this study was to analyze global gene expression in specific populations of somatosensory neurons in the periphery, including major, non-overlapping populations that include nociceptors, pruriceptors, and prorioceptors. The mammalian somatosensory nervous system encodes the perception of specific environmental stimuli. The dorsal root ganglion (DRG) contains distinct somatosensory neuron subtypes that innervate diverse peripheral tissues, mediating the detection of thermal, mechanical, proprioceptive, pruriceptive, and nociceptive stimuli. We purified discrete subtypes of mouse DRG somatosensory neurons by flow cytometry using fluorescently labeled mouse lines (SNS-Cre/TdTomato, Parv-Cre/TdTomato) in combination with Isolectin B4-FITC surface staining (IB4). This allowed identification of transcriptional differences between these major populations, revealing enrichment of voltage-gated ion channels, TRP channels, G-protein coupled receptors, transcription factors, and other functionally important classes of genes within specific somatosensory neuron subsets. SNS-Cre mice were bred with Rosa26-TdTomato mice to generate SNS-Cre/TdTomato reporter mice. Parv-Cre mice were bred with Rosa26-TdTomato mice to generate Parv-Cre/TdTomato mice. Isolectin B4-FITC was used to stain the surface of SNS-Cre/TdTomato reporter mice. We used these strategies of fluorescent labeling to purify distinct murine sensory neuron subsets from the dorsal root ganglia (DRG) by fluorescence activated cell sorting (FACS). Neurons were sorted directly in Qiazol for total RNA extraction and microarray analysis. Whole DRG tissue was also included for transcriptome analysis to compare with purified neuronal populations.

2014-12-23 | E-GEOD-55114 | biostudies-arrayexpress

Chip-seq For Meis2 on embryonic (E16) and adult DRG

Project description:The goal was to identify DNA binding sites for the transcription factor Meis2 in native embryonic day 16 (E16) and adult sensory neurons from dorsal root ganglion (DRGs).

2021-12-01 | GSE169319 | GEO

Somatosensory Neuron Types Identified by High-Coverage Single-Cell RNA-Sequencing and Functional Heterogeneity

Project description:Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here we classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 ± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases.

2015-12-10 | GSE63576 | GEO

Sc-RNA seq for intrinsic mechanisms of distinct axonal growth capacity in different peripheral sensory neuron subtypes

Project description:Dorsal root ganglion neurons are the primary neurons of the sensory afferent pathway and are a heterogeneous population. Dorsal root ganglion neurons exhibit a wide range of terminal morphologies, complex central projection patterns, and different physiological properties, which allow them to adapt to various sensory stimulation modalities and transmit the corresponding sensory information to the central nervous system. Here, we used single-cell sequencing technology to explore the mechanisms behind the differences in axonal lengths in DRG neurons cultured in vitro. The single-cell sequencing data grouped by axon length were compared and analyzed to find core genes that may be closely related to axon length in a list of differentially expressed genes that significantly change with axon length; as well as to explore whether these genes also play an important role in the process of axon regeneration after peripheral nerve injury.

2022-10-01 | GSE205983 | GEO

Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [humanDRG]

Project description:Sensory neurons of the dorsal root ganglion (DRG) play a crucial role in maintaining tissue homeostasis by sensing and initiating responses to stimuli. While most preclinical studies of DRGs are conducted in rodents, much less is known about the mechanisms of sensory perception in primates. We generated a transcriptome atlas for mouse, guinea pig, cynomolgus monkey, and human DRGs using a framework that implements a common laboratory workflow (i.e sequencing technologies, laboratory protocols, and sample archival methods) and multiple data-integration approaches to generate accurate cross-species mappings of sensory neuron subtypes.

2022-12-21 | GSE201586 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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