Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Coupled electrophysiological recording and single-cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation

PROVIDER: PRJNA310792 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3144410.fastq.gz	Fastqsanger.gz
	SRR3144420.fastq.gz	Fastqsanger.gz
	SRR3144411.fastq.gz	Fastqsanger.gz
	SRR3144412.fastq.gz	Fastqsanger.gz
	SRR3144422.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Coupled electrophysiological recording and single-cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation

Project description:The mammalian brain is heterogeneous, containing billions of neurons and trillions of synapses forming various neural circuitries, through which sense, movement, thought, and emotion are generated. The cellular heterogeneity of the brain has made it difficult to study the molecular logic of neural circuitry wiring, pruning, activation, and plasticity, until recently, transcriptome analyses with single-cell resolution makes decoding of gene regulatory networks underlying aforementioned circuitry properties possible. Here, we report success in performing both electrophysiological and whole-genome transcriptome analyses on single human neurons in culture. Using Weighted Gene Coexpression Network Analyses (WGCNA), we identified gene clusters highly correlated with neuronal maturation judged by electrophysiological characteristics. A tight link between neuronal maturation and genes involved in ubiquitination and mitochondrial function was revealed. Moreover, we identified a list of candidate genes, which could potentially serve as biomarkers for neuronal maturation. Coupled electrophysiological recording and single-cell transcriptome analysis will serve as powerful tools in the future to unveil molecular logics for neural circuitry functions.

2016-05-26 | GSE77564 | GEO

In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy

Project description:In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy

| PRJNA672925 | ENA

Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking

Project description:Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking

| PRJNA1146327 | ENA

Morphological, electrophysiological and transcriptomic profiling of single neurons using Patch-seq

Project description:The mammalian neocortex is a layered sheet of neural tissue that mediates complex cognitive processes including perception and cognition. Despite its importance, we still lack detailed knowledge of the cellular components of the neocortex. Integrating morphological, electrophysiological and molecular classification schemes into a common framework for defining cell types is challenging due to the limited scope of most single-cell analyses. Here, we developed a protocol for high-throughput electrophysiological and transcriptomic analysis of single neurons that combines whole-cell recordings and single-cell RNA-sequencing, which we call Patch-seq. Using this approach, we fully characterized the electrophysiological and molecular profiles of ~50 neocortical neurons, and show that gene expression patterns can be used to infer the morphological and physiological properties of individual neurons and their corresponding cell type. Our results shed light on the molecular underpinnings of neuronal diversity and demonstrate a path forward for comprehensive cell type characterization in the nervous system.

2016-01-25 | E-MTAB-4092 | biostudies-arrayexpress

In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (totalRNA)

Project description:In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (totalRNA)

| PRJNA672928 | ENA

In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (smallRNA)

Project description:In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (smallRNA)

| PRJNA672929 | ENA

Project description:MOLECULAR MECHANISMS UNDERLYING MITOCHONDRIAL DYSFUNCTION

| PRJNA1002987 | ENA

Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation

Project description:NGN2-driven iPSC-to-neuron conversion is a popular method for human neurological disease modeling. In this study, we report a fully standardized approach for generating functional excitatory cortical neurons. This method utilizes clonal, targeted-engineered iPSC lines and employs fully defined reagents. We demonstrate that our protocol generates consistent excitatory cortical neurons at scale. Comprehensive temporal omics, electrophysiological, and morphological profilings indicate the continued progression of neuronal maturation for at least 150 days. Deep quantitative characterizations through transcriptomic, imaging, and functional assays reveal coordinated actions of multiple pathways driving neuronal maturation. The neurons express the majority of the key risk genes in Alzheimer's disease, Parkinson's disease, and autism, demonstrating the relevance of our protocol in modeling human neurological disorders. This well-defined method, profiling data, and functional characterization provide a solid and reliable framework for developing human in vitro neuronal models for disease modeling.

2023-10-18 | MSV000093150 | MassIVE

smalRNA seq of IPSC-cardiomyocytes treated with exosomes before hypoxic stiumli

Project description:This experiment aimed to investigate whether exosomess released by IPSC-cardiomyocytes during hypoxia can positively influence cardiac electrophysiology and miRNA expression during hypoxic stress. A multielectrode array (MEA) system was used as an in vitro method of recording real-time cardiac electrophysiological activity, highlighting the biological effects facilitated by exosomes. Additionally, miRNA-sequencing was performed to compare miRNA expressions in exosome-preconditioned and non-preconditioned IPSC-cardiomyocytes, elucidating important modulators of cardiac electrophysiology.

2024-04-01 | E-MTAB-13912 | biostudies-arrayexpress

Cortical bulk RNA sequencing of the microglia specific TREM2 inducible mouse models

Project description:We performed brain bulk RNA-seq aiming to study how microglia TREM2-WT or TREM2-R47H expression affect the overall brain transcriptomic profiles. Using WGCNA gene network analysis, we found the presynaptic transmission pathway was dysregulated after TREM2-R47H expression, not TREM2-WT. This finding was consistent with the impaired presynaptic transmission detected by electrophysiological recording in TREM2-R47H expressing mice. In addition, dysregulated circadian pathways were also identified in TREM2-R47H mice, not in TREM2-WT mice. Altogether, our bulk RNA-seq results provide additional evidence at transcriptomics level that TREM2-R47H expression in microglia affects neuronal functions and brain networks.

2020-11-11 | GSE161223 | 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