Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-coding RNAs shape cortical neurons developmental trajectories

ABSTRACT: Non-coding RNAs shape cortical neurons developmental trajectories

PROVIDER: PRJNA669828 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12837300.fastq.gz	Fastqsanger.gz
	SRR12837400.fastq.gz	Fastqsanger.gz
	SRR12837500.fastq.gz	Fastqsanger.gz
	SRR12837600.fastq.gz	Fastqsanger.gz
	SRR12837700.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 2524

Similar Datasets

Non-coding RNAs shape cortical neurons developmental trajectories

Project description:A hallmark of cortical evolution is the high dynamic subventricular zone (SVZ) expansion, where basal progenitors (BPs) amplify and neuronal transcriptional programs unfold. How non-coding molecular factors such as microRNAs influence these developmental trajectories and regulate the acquisition of cortical type identities is largely unknown. Here we demonstrate that miR-137 and miR-122 regulate the positioning and identity features of superficial layer cortical neurons by acting at distinct steps of their developmental trajectories. MiR-137 sustains basal progenitor amplification by reverting their neurogenic commitment and inducing high proliferative state upregulating Cd63 and inhibiting Myt1l. Cd63 is an extra-cellular matrix (ECM) receptor which interacts with b3- and 1-integrin pathways to promote proliferation, while Myt1l is a transcription factor that promotes and sustains neuronal fate. The BPs amplification by miR-137 is converted in the promotion of intracortical projecting neuron (ICPN) identity and L2/3 expansion. As opposed to miR-137, miR-122 acts postmitotically, affecting the bioelectrical properties, the calcium and cytoskeleton dynamics of newborn neurons as well as their transcriptional program, leading to a persistent molecular immaturity across time. Overall, these findings reveal that miR-137 and miR-122 are key regulators of the developmental trajectory of cortical neurons across evolution.

2022-03-09 | GSE159596 | GEO

Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories

Project description:The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge through the implementation of different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons, as they represent a relatively small proportion of all cortical cells, migrate tangentially from their embryonic origin to the cerebral cortex, and have a protracted development. Here we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells, the most diverse subclass of inhibitory neurons in the mouse cerebral cortex. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is further refined during early postanal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons. Thus, the diversification of SST+ inhibitory neurons involves a temporal cascade of unique molecular programs driving their divergent developmental trajectories.

2023-11-01 | GSE217065 | GEO

Transcriptome analysis of mouse cortical development and characterization of long non-coding RNAs

Project description:Cortical neural progenitor cells (NPCs) change their competency over time during development, giving rise to distinct cell types sequentially. Many genes that govern cortical development are now known, but it remains elusive how their temporal expression is controlled. Recently, long non-coding RNAs are found to be essential for cell-fate specification and precise gene regulation in many developmental events. In this study, strand-specific RNA sequencing studies unveil large amount of long non-coding RNAs are actively and differentially expressed across mouse cortical development. Integration of RNA sequencing data from key stages of developing mouse cortex enables us to cluster coding and non-coding transcripts into co-expression “modules” to infer functional relationships. Intriguingly, the cortical transcriptome undergoes significant changes in early mouse neurogenesis. Cortical long non-coding RNAs tends to be transcribed from genomic loci adjacent to protein-coding genes related to neural development. Finally, we found large amount of predicted enhancer regions are able to transcribe RNAs. This study will help us better understand molecularly how cortical NPCs specify their fates during development, especially roles of lncRNAs in this process.

2019-02-26 | GSE55600 | GEO

Type-I-interferon-responsive microglia shape cortical development and behavior

Project description:Type-I-interferon-responsive microglia shape cortical development and behavior

| PRJNA724035 | ENA

Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks

Project description:Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks

| PRJNA1037169 | ENA

CRISPR activation of long non-coding RNAs transiently expressed during cortical neuron differentiation associated with Field, et al, Stem Cell Reports 2018

Project description:4 transiently expressed long non-coding RNAs that were identified in human and non-human primate cortical organoid differentiation were activated out of context in HEK293FT cells using CRISPRa.

2018-10-04 | GSE120702 | GEO

Genomics of Developmental Trajectories in Twins

Project description:Genomics of Developmental Trajectories in Twins

| PRJNA171522 | ENA

Enhancer RNAs make multivalent interactions with NELF to stimulate Pol II pause release [SHAPE]

Project description:A SHAPE-MaP structure probing experiment was performed on 40 eRNAs. The eRNA transcription start sites (TSSs) were identified by 5'-ExoSeq. The 5' end fragment (1-200 nucleotides) of each eRNA was cloned from mouse cortical neurons and the eRNAs were produced by in vitro transcription. Each eRNA was treated in one sample with DMSO (control) and in a second sample with the SHAPE reagent 1-Methyl-7-nitroisatoic anhydride (1M7). The 1M7 chemical will react preferentially with the ribose 2'OH of the flexible nucleotides in single stranded regions and the produced adduct will lead to mutations during reverse transcription.

2022-03-08 | GSE163112 | GEO

CHD8 haploinsufficiency alters the developmental trajectories of human excitatory and inhibitory neurons linking autism phenotypes with transient cellular defects

Project description:Chromodomain helicase DNA-binding 8 (CHD8) is one of the most frequently mutated genes causative of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly and hence implicates cortical abnormalities in this form of ASD, the neurodevelopmental impact of human CHD8 haploinsufficiency remains unexplored. Here we combined human cerebral organoids and single cell transcriptomics to define the effect of ASD-linked CHD8 mutations on human cortical development. We found that CHD8 haploinsufficiency causes a major disruption of neurodevelopmental trajectories with an accelerated generation of inhibitory neurons and a delayed production of excitatory neurons alongside the ensuing protraction of the proliferation phase. This imbalance may contribute to the significant enlargement of cerebral organoids in line with the macrocephaly observed in patients with CHD8 mutations. By adopting an isogenic design of patient-specific mutations and mosaic cerebral organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Finally, our results assign different CHD8-dependent molecular defects to particular cell types, pointing to an abnormal and extended program of proliferation and alternative splicing specifically affected in, respectively, the radial glial and immature neuronal compartments. By identifying temporally restricted cell-type specific effects of human CHD8 mutations, our study uncovers developmental alterations as reproducible endophenotypes for neurodevelopmental disease modelling.

2024-01-27 | E-MTAB-11406 | biostudies-arrayexpress

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

Project description:During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes. This SuperSeries is composed of the SubSeries listed below.

2018-04-27 | GSE106587 | 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