Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

ABSTRACT: Neocortical cellular diversity emerges gradually during development. Cell-extrinsic interactions shape this extended maturation, yet cell-type-specific dependence on such cues has not been systematically examined. To address this, we compared how cell identity and diversity unfolds in different conditions during neocortical development. Conditions were modified in vivo using genetically modified mice models in which position or innervation are altered and in vitro using two-dimensional cultures. This approach revealed a molecular hierarchy in which cell class-distinguishing features emerge first, followed by subclass- and type-related characteristics. Acquisition of cellular identity and diversity remained stable across in vivo models. In contrast, in vitro glutamatergic neurons showed decreased expression of identity-defining genes, reduced diversity and alterations in connectivity. Cellular identity and diversity were closest to in vivo values in organotypic cultures. These findings reveal population-specific responses to environmental conditions and highlight the role of extracellular context in shaping cell diversity in the maturing neocortex.

ORGANISM(S): Mus musculus

PROVIDER: GSE307040 | GEO | 2025/09/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cell-extrinsic controls over neocortical neuron fate and diversity [PatchSeq]

Project description:Neocortical cellular diversity emerges gradually during development. Cell-extrinsic interactions shape this extended maturation, yet cell-type-specific dependence on such cues has not been systematically examined. To address this, we compared how cell identity and diversity unfolds in different conditions during neocortical development. Conditions were modified in vivo using genetically modified mice models in which position or innervation are altered and in vitro using two-dimensional cultures. This approach revealed a molecular hierarchy in which cell class-distinguishing features emerge first, followed by subclass- and type-related characteristics. Acquisition of cellular identity and diversity remained stable across in vivo models. In contrast, in vitro glutamatergic neurons showed decreased expression of identity-defining genes, reduced diversity and alterations in connectivity. Cellular identity and diversity were closest to in vivo values in organotypic cultures. These findings reveal population-specific responses to environmental conditions and highlight the role of extracellular context in shaping cell diversity in the maturing neocortex.

2025-09-18 | GSE307039 | GEO

Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

Project description:Cell-extrinsic controls over neocortical neuron fate and diversity [snRNAseq]

| PRJNA1314165 | ENA

snRNAseq in human fetal neocortex

Project description:Abnormalities in neocortical and synaptic development have been associated with neurodevelopmental disorders. However, the molecular and cellular mechanisms regulating the formation of the initial synapses in an evolutionary advanced neocortical layer, the subplate (SP), are poorly understood. Our snRNAseq screen of human prefrontal neocortices from early (11/12 PCW), mid (14/15 PCW) to late (17/18 PCW) fetal developmental stages revealed the bipartite-to-tripartite differentiation of SP neuronal subclasses. Using polysome profiling with RNAseq, we report for the first time a set of mRNAs undergoing translational control in cellular subclasses of developing human prefrontal neocortices, including SP neurons. By examining both mouse and human neocortex, we further found that an autism spectrum disorder (ASD)-risk gene and RNA binding protein CUGBP Elav-Like Family Member 4 (CELF4) is selectively expressed in the neurons of two synapse-enriched compartments, the SP and the marginal zone. Furthermore, CELF4 binds mRNA targets that are encoded by the synaptic genes associated with ASD and adverse neurodevelopmental outcomes; albeit in an evolutionarily advanced fashion between mouse and human synaptic mRNAs. The selective forebrain Celf4 deletion from developing mouse cortical neurons disrupts the balance of SP synapses in a gender-specific fashion. Taken together, our results underscore the importance of RNA binding proteins and mRNA translation in evolutionarily advanced synaptic development, as well as their possible contribution to gender specific protein synthesis and vulnerability.

2023-08-07 | GSE214532 | GEO

Gene expression profiles of control versus Prdm16-overexpressing cells

Project description:Embryonic neocortical cells were isolated from E14.5 WT mice, followed by TrypLE Express treatment and trituration to generate a single-cell suspension. Plasmid DNA was introduced into primary neocortical cells using Neon Transfection System. Next, neocortical neurospheres were cultured in serum-free media containing, then control and Prdm16-overexpressing cells were corrected after GFP sorting of 1 day cultures. We found that marked upregulation of modulators of mitochondrial metabolism and ROS balance in Prdm16 GOF cells

2017-04-03 | E-MTAB-5646 | biostudies-arrayexpress

Brain-wide neuronal circuit connectome of human glioblastoma

Project description:This study explores the circuit integration of human glioblastoma organoids (GBOs) in vivo in the adult mouse brain. We performed single cell RNA sequencing (scRNA-seq) to understand the cell state diversity of malignant tumor cells in GBOs at baseline and after stimulation by 1 mM acetylcholine (ACh) for 1 hour. Sliced neocortical organoids (SNOs) were also sequenced to study gene expression properties of neural stem cells (NSCs).

2024-12-20 | GSE274460 | GEO

Stem cell derived spinal cord chips reproduce disease biomarkers in sporadic ALS patients [snRNAseq]

Project description:Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder with complex origins. Familial monogenetic causes of ALS make up a small percentage of patients overall, and the cause of the majority of idiopathic (sporadic) form remains unknown. Frequently utilized for disease modeling, human induced pluripotent stem cell (iPSC)-derived motor neuron cultures lack cellular maturity in vitro and rarely recapitulate clinically relevant phenotypes of ALS. Microfluidic organ-on-chip systems enable co-culture of multiple disease-relevant cell types and enhance cellular maturity. Here, we describe the generation of spinal cord (SC)-chips from 8 sporadic ALS (sALS) patients and 10 non-diseased controls. Transcriptomic and proteomic analyses of SC-Chips revealed changes in expression of targets known to be disrupted in ALS patients. Particularly, intermediate filaments (IF) neurofilament heavy (NEFH), medium (NEFM), and light (NEFL) were upregulated in SC-Chips from sALS patients. Single nuclei RNAseq (sNucseq) of SC-Chips revealed two subpopulations of motor neurons and cell-specific changes related to ALS pathogenesis and mimicking conditions in vivo.

2025-06-24 | GSE255605 | GEO

DLG2 knockout reveals neurogenic transcriptional programs underlying neuropsychiatric disorders and cognition

Project description:A complex train of events unfolds during brain development, guided by activation/repression of gene expression programs. It remains unclear how this process is disrupted in disease. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. This reveals a cascade of transcriptional programs activated during early corticoneurogenesis in vitro and in vivo. Genetic variation in these programs is robustly associated with neuropsychiatric disorders and cognitive function, with variants concentrated in loss-of-function intolerant genes. Neurogenic programs also capture schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways activated during pre-natal development underlie disease-relevant deficits in mature neuronal function. Down-regulation of these programs in DLG2-/- lines delays expression of cell-type identity and impairs neuronal migration, morphology and action potential generation, validating predicted deficits. These data implicate specific cellular pathways underlying neurodevelopment in the aetiology of multiple neuropsychiatric disorders and cognition.

2021-11-11 | PXD029526 | Pride

Single Cell Analysis in trisomic tissues and organoids

Project description:Cortical organoids generated from mESC from a Down Syndrome (DS) mouse model (Ts65Dn) were dissociated for single cell sequencing to understand whether differential gene expression in DS brains affects cell diversity and how the molecular events that control the development of these diverse types of neocortical neurons are affected by the trisomy. These results were generated in parallel to a single cell experiment in forebrain fetal tissue from WT and Ts65Dn mice.

2023-03-15 | E-MTAB-12827 | biostudies-arrayexpress

Heterogeneous fates of simultaneously-born neurons in the cortical ventricular zone

Project description:Neocortical excitatory neurons belong to diverse cell types, which can be distinguished by their dates of birth, laminar location, connectivity and molecular identities. During embryogenesis, apical progenitors (APs) located in the ventricular zone first give birth to deep-layer neurons, and next to superficial-layer neurons. While the overall sequential construction of neocortical layers is well-established, whether multiple neuron types are produced by APs at single time points of corticogenesis is unknown. To address this question, here we used FlashTag to fate-map simultaneously-born (i.e. isochronic) cohorts of AP-born neurons at successive stages of corticogenesis. We reveal that early in corticogenesis, isochronic neurons differentiate into heterogeneous laminar, hodological and molecular cell types. Later on, instead, simultaneously-born neurons have more homogeneous fates. Using single-cell gene expression analyses, we identify an early postmitotic surge in the molecular heterogeneity of nascent neurons during which some early-born neurons initiate and partially execute late-born neuron transcriptional programs. Together, these findings suggest that as corticogenesis unfolds, mechanisms allowing increased homogeneity in neuronal output are progressively implemented, resulting in progressively more predictable neuronal identities.

2022-04-20 | GSE191205 | GEO

Gene expression data from primary mouse neocortical cultures

Project description:Primary murine neocortical cultures are a common model for investigating fundamental attributes of neuronal signalling. Here we utilized an Affymetrix GeneChip platform to measure expression of various genes in vitro in order to chracterize our cortical cultures.

2022-11-23 | GSE218028 | 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