Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptomic and epigenetic profiling of mouse myenteric plexus glial cells

ABSTRACT: This study was undertaken to define the molecular subtypes of myenteric plexus glial cells in mice, and to understand the molecular basis for glial cells’ capacity to become neurons. Methods: We performed single-cell RNA sequencing and single-nucleus ATAC sequencing of enteric neurons from small intestine at the adolescent mice (on or near postnatal day of life 14). We also performed both single-cell RNA sequencing and single-nucleus ATAC sequencing on 3-dimensional neurosphere cultures. Results: We identify numerous distinct transcriptional subgroups of myenteric plexus glial cells, including cells expressing genes associated with neuronal differentiation. Epigenetic analysis shows distinct chromatin accessibility profiles that correlate with gene expression patterns. Glial cells maintain open chromatin at gene loci associated with neuronal fate. 3-dimensional cultures provide a niche for active neurogenesis. Chromatin closes at glial-associate loci during neurogenesis. Conclusion: Utilizing single-cell RNA sequencing and single-nucleus ATAC sequencing, we identify myenteric glial cell subtypes and uncover a molecular basis for a glial-to-neuronal fate transition.

ORGANISM(S): Mus musculus

PROVIDER: GSE184981 | GEO | 2023/03/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Enteric nervous system: timecourse analysis of longitudinal muscle and myenteric plexus (LMMP) in mice

Project description:Samples of dissociated mouse small intestinal longitudinal muscle-myenteric plexus were prepared from post natal day 10 (P10), P20, and P60, each with two biological replicates. Samples were run through the 10x Chromium 3' Single Cell Gene Expression platform v3.1

2023-02-06 | GSE213604 | GEO

Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Human Enteric Ganglia]

Project description:The data provided here were used to generate a comprehensive transcriptome atlas for the human myenteric plexus from healthy human adults

2020-10-12 | GSE153198 | GEO

Neuronal Development And The Onset Of Electrical Activity In The Human Enteric Nervous System

Project description:Objective: To assess the development of neuronal subtypes and the emergence of evoked electrical activity within the developing human ENS. Methods: Human foetal gut samples were obtaining via the MRC-Wellcome Trust Human Developmental Biology Resource (UK). Characterisation of the developing ENS was performed by immunohistochemistry, calcium imaging, RNAseq and qRT-PCR Results: Human foetal colon samples displayed robust Tuj1 immunohistochemistry by embryonic week (EW) 12 with a dense neuronal network at the level of the myenteric plexus. At EW12 expression of excitatory neurotransmitter markers (VAChT and Sub P) was observed. By contrast, inhibitory neurotransmitter markers (nNOS and VIP) were not observed until EW14. Co-labeling with synaptic markers (SYN1/SNAP-25) demonstrated the development of synaptic contacts by EW12. However, electrical train stimulation (40V,2s,20Hz of 300?s electrical pulses) did not evoke activity within the myenteric plexus of EW12 foetal gut (n=0/3). Similarly, the majority of EW14 gut tissues assessed (80%), demonstrated no response to electrical stimulation (n=4/5). Interestingly, at EW16 Tuj1+ expression, in the myenteric plexus, was observed within discrete ganglia and was combined with the emergence of calcium transients (F/F0=1.273±0.024;n=3), upon electrical stimulation (n=3/3), which were abolished after the addition of 1uM TTX (n=3/3). RNAseq and qRT-PCR analysis between EW12-16 revealed increases in expression in genes involved in neurotransmission and action potential generation including SCN9A and KCNQ3. Conclusion: Here we demonstrate the temporal development of human enteric neuronal subtypes from EW12-14 and the subsequent emergence of coordinated electrical activity within the human foetal ENS at approximately EW16.

2019-02-20 | GSE111307 | GEO

Control of neurogenic competence in mammalian hypothalamic tanycytes [RNA-seq]

Project description:Hypothalamic tanycytes, radial glial cells that share many features with neuronal progenitors, can generate small numbers of neurons in the postnatal hypothalamus, but the identity of these neurons and the molecular mechanisms that control tanycyte-derived neurogenesis are unknown. We report that tanycyte-specific disruption of the NFI family of transcription factors (Nfia/b/x) stimulates proliferation and tanycyte-derived neurogenesis. Single-cell RNA- and ATAC-Seq analysis reveals that NFI factors repress Shh and Wnt signaling in tanycytes, and small molecule inhibition of these pathways blocks proliferation and tanycyte-derived neurogenesis in Nfia/b/x-deficient mice. We show that Nfia/b/x-deficient tanycytes give rise to multiple mediobasal hypothalamic neuronal subtypes that can mature, integrate into hypothalamic circuitry, and selectively respond to changes in internal states. These findings identify molecular mechanisms controlling tanycyte-derived neurogenesis that can potentially be targeted to selectively remodel hypothalamic neural circuitry controlling homeostatic physiological processes.

2020-10-30 | GSE160377 | GEO

Control of neurogenic competence in mammalian hypothalamic tanycytes [ATAC-seq]

2020-10-30 | GSE160375 | GEO

Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development

Project description:For most multigenic disorders, clinical manifestation (penetrance) and presentation (expressivity) are likely to be an outcome of genetic interaction between multiple susceptibility genes. Here, using gene knockouts in mice we evaluated genetic interaction between loss of Ret and loss of Sema3d, two Hirschsprung disease (HSCR) susceptibility genes. We intercrossed Ret and Sema3d double null heterozygotes to generate mice with the nine possible genotypes and assessed survival by counting various genotypes, myenteric plexus development by acetylcholinesterase (AchE) staining and embryonic day 12.5 (E12.5) gut transcriptome by RNA-sequencing. Survival rates of Ret wildtype, null heterozygote and null homozygote mice at E12.5, birth and weaning were not influenced by the genotypes at Sema3d locus and vice-versa. Loss of myenteric plexus was observed only in all Ret null homozygotes, irrespective of the genotypes at Sema3d locus, and Sema3d null heterozygote and homozygote mice had normal gut innervation. As compared to wildtype mice gut gene expression, loss of Ret in null homozygotes led to differential expression of ~300 genes, whereas loss of Sema3d in null homozygotes had no major consequence and there was no evidence supporting major interaction between the two genes influencing gut transcriptome. Overall, given the null alleles and phenotypic assays used, we did not find evidence for genetic interaction between Ret and Sema3d affecting survival, myenteric plexus formation or gut transcriptome.

2017-03-28 | GSE89627 | GEO

Bulk RNA-sequencing of self-maintaining versus monocyte-replaced gut macrophages

Project description:Self-maintaining gMacs are present in the submucosal and myenteric plexus of the intestine where they maintain enteric neurons and submucosal vasculature YFP-positive and YFP-negative CD11b+, CD64+ macrophages were sorted from lamina propria and muscularis externa of Cx3cr1CreERT2.Rosa26-LSL-YFP animals, 35 weeks after tamoxifen administration. Four biological replicates each. YFP-positive and YFP-negative were compared within lamina propria and muscularis externa

2018-07-30 | E-MTAB-6977 | biostudies-arrayexpress

Cellular Taxonomy of the Adult Human Spinal Cord

Project description:This study generates a census of cell signatures using single-nucleus RNA-sequencing data from dissociated lumbar human spinal cord. Nuclei were isolated using a triton-based dissociation protocol, processed using the 10x Genomic Chromium 3' platform (v3), and clustered into major cell classes as well as subtypes within each neuronal and glial class.

2023-01-31 | GSE190442 | GEO

scRNA-sequencing reveals new enteric nervous system roles for GDNF, NRTN, and TBX3

Project description:Bowel function requires coordinated activity of many enteric neuron subtypes. Clear definition of subtype-specific gene expression may facilitate molecular diagnoses for bowel motility disorders. Using adult mouse colon RNAseq data from 635 myenteric neurons and 707 E17.5 neurons, we defined seven adult myenteric neuron subtypes, eight E17.5 neuron subtypes and hundreds of differentially-expressed genes. Manually dissected human colon myenteric plexus yielded data from 48 neurons, 3798 glia, 5568 smooth muscle, 377 interstitial cells, and 2153 macrophages. Immunohistochemistry demonstrated differential protein abundance for BNC2, PBX3, RBFOX1, TBX2, and TBX3 in enteric neuron subtypes. Conditional Tbx3 loss reduced NOS1-expressing myenteric neurons. Differential Gfra1 and Gfra2 expression coupled with calcium imaging revealed that GDNF and neurturin acutely and differentially regulate activity of ~50% of myenteric neurons with distinct effects on smooth muscle contractions. This insight into enteric nervous system biology provides a foundation for future studies of bowel motility disorders.

2021-01-01 | GSE156905 | GEO

Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

Project description:This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

2023-08-07 | GSE233754 | 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