Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression changes in differentiated cortical neurospheres pre-exposed to ethanol

ABSTRACT: Cerebral cortical-derived neurosphere cultures were exposed to ethanol to model heavy alcohol exposure during the period of cortical neurogenesis Keywords: Compared differentiated neurospheres pre-exposed to ethanol to untreated differentiated neurospheres

ORGANISM(S): Mus musculus

PROVIDER: GSE5152 | GEO | 2006/09/30

SECONDARY ACCESSION(S): PRJNA96551

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression changes in fetuses exposed to ethanol in utero

Project description:Timed pregnant C57Bl6 mice were exposed to ethanol during a critical period, gestational day 15 to 18, of cerebral cortical development to identify gene expression changes in the cerebral cortex of developing fetus due to this ethanol exposure Keywords: Compared animals exposed to ethanol (alcohol fed group) to a pair-fed control group and both groups were normalized to a control group (animals fed adlibitum)

2006-10-31 | GSE5186 | GEO

Analysis of microRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using small RNA sequencing

Project description:Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate microRNA expression changes in the brains of subjects with alcohol use disorder (AUD). Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for small RNA sequencing. The sequence reads were processed using the Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow. Ethanol-induced miRNA transcriptomic changes were analyzed by the Limma-Voom method. Results: A 7-day ethanol exposure led to differential expression of six miRNAs (absolute FC>2.0 & P<0.05) in hESC-derived cortical interneurons. Three miRNAs were upregulated (>2-fold increase & P<0.05), while three other miRNAs were downregulated (> 2-fold decrease & P < 0.05) due to ethanol exposure. Conclusions: The hESC-derived neural cell model study can partially validate miRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.

2021-10-13 | GSE181050 | GEO

Mus musculus

Project description:Gene expression changes in differentiated cortical neurospheres pre-exposed to ethanol

| PRJNA96551 | ENA

Analysis of mRNA transcriptomic changes in ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons using ribosome depletion RNA sequencing

Project description:Purpose: The goal of this study to use ethanol-exposed human embryonic stem cell (hESC)-derived neural cells as models to investigate mRNA expression changes in the brains of subjects with alcohol use disorder (AUD). Methods: hESCs were differentiated into neural cells (mainly cortical interneurons), which were then cultured in media with or without ethanol (50-100 mM) for 7 days (by duplicate experiments). Total RNAs were extracted from hESC-derived neural cells (with or without ethanol exposure) for mRNA sequencing. The sequence reads were processed using the RNA-seq processing pipeline Pipeliner [Front Genet. 2019; 10:614] workflow. Ethanol-induced mRNA transcriptomic changes were analyzed by the Limma-Voom method. Results: When the significance level was set at FC>2.0 & P<0.01, 19 coding genes showed differential expression, and all of them were downregulated after a 7-day ethanol exposure. Conclusions: The hESC-derived neural cell model study can partially validate mRNA transcriptomic changes in postmortem brains of subjects with alcohol use disorder.

2021-10-13 | GSE181049 | GEO

Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres

Project description:Axon guidance is required for the establishment of brain circuits. Whether much of the molecular basis of axon guidance is known from animal models, the molecular machinery coordinating axon growth and pathfinding in humans remains to be elucidated. The use of induced pluripotent stem cells (iPSC) from human donors has revolutionized in vitro studies of the human brain. iPSC can be differentiated into neuronal stem cells which can be used to generate neural tissue-like cultures, known as neurospheres, that reproduce, in many aspects, the cell types and molecules present in the brain. Here, we analyzed quantitative changes in the proteome of neurospheres during differentiation. Relative quantification was performed at early time points during differentiation using iTRAQ-based labeling and LC-MS/MS analysis. We identified 6438 proteins, from which 433 were downregulated and 479 were upregulated during differentiation. We show that human neurospheres have a molecular profile that correlates to the fetal brain. During differentiation, upregulated pathways are related to neuronal development and differentiation, cell adhesion and axonal guidance whereas cell proliferation pathways were downregulated. We developed a functional assay to check for neurite outgrowth in neurospheres and confirmed that neurite outgrowth potential is increased after 10 days of differentiation and is enhanced by increasing cyclic AMP levels. The proteins identified here represent a resource to monitor neurosphere differentiation and coupled to the neurite outgrowth assay can be used to functionally explore neurological disorders using human neurospheres as a model.

2021-02-25 | PXD024177 | Pride

Transcription profiling of CD133/Prominin positive neurospheres

Project description:To identify expression of hematopoetic stem cell antigens in cerebral cortical derived neurospheres Keywords: Compared CD133 positive neurospheres to control GFP-positive neurospheres

2006-10-01 | GSE5171 | GEO

Mouse cerebellar libraries:Ethanol-treated and controls

Project description:P300 and P720 C57BL6/J male mice were exposed to ethanol vapor (95% w/v) for 3 hours each day for a total of 5 days. Blood alcohol levels in the ethanol treated animals was 3.0mg/ml. Controls at P300 and P720 were included. Keywords: SAGE-dose response

2006-11-22 | GSE4520 | GEO

E14.5 mouse cortical neurospheres in response to Fezf2 over-expression

Project description:RNA Sequencing of E14.5 mouse cortical neurospheres in response to Fezf2 over-expression 2 replicates each of GFP-transfected or Fezf2/GFP-transfected E14.5 mouse cortical neurospheres. Paired-end sequencing 101bp.

2014-07-06 | E-GEOD-56446 | biostudies-arrayexpress

ATAC-seq for Pantr2 knockout cortical neurospheres

Project description:We used assay for transposase accessible chromatin with sequencing (ATAC-seq) to discover changes in chromatin accessibility in Pantr2 KO cortical neurospheres

2022-08-02 | GSE210135 | GEO

Microarray analysis of differentiation of human glioblastoma neurospheres

Project description:Brain tumor neurospheres (BTCSs) are cancer cells with neural stem cell-like properties found in the fatal brain tumor glioblastoma multiforme (GBM). These cells account for less than 1% of total tumor cells, are poorly differentiated and are believed to be involved in tumor induction, progression, treatment resistance and relapse. Specific miRNAs play important roles in modulating the proliferation and differentiation of neural stem cells, therefore, we aimed to identify miRNAs controlling differentiation in GBM-BTSCs through high throughput screening miRNA array profiling. We compared the miRNA expression profiles at the neurosphere state and upon 4 and 14days of differentiation by using LIMMA, finding 21 differentially expressed miRNAs : hsa-miR-103, hsa-miR-106a, hsa-miR-106b, hsa-miR-15b, hsa-miR-17, hsa-miR-19a, hsa-miR-20a, hsa-miR-25, hsa-miR-301a and hsa-miR-93 were found up-regulated upon differentiation, while hsa-miR-100, hsa-miR-1259, hsa-miR-21, hsa-miR-22, hsa-miR-221, hsa-miR-222, hsa-miR-23b, hsa-miR-27a, hsa-miR-27b, hsa-miR-29a and hsa-miR-29b were down-regulated. Expression of 11 of the 21 miRNAs was examined by qPCR and 7 of them were validated: hsa-miR-21, hsa-miR-29a, hsa-miR-29b, hsa-miR-221 and hsa-miR-222 increased their expression upon differentiation, while hsa-miR-93 and hsa-miR-106a were inhibited. Functional studies demonstrated that miR-21 over-expression induced the expression of glial and/or neuronal cell markers in the neurospheres, possibly due to SPRY1 targeting by miR-21 in these cells, while miR-221 and miR-222 inhibition at the differentiated state reduced the expression of those differentiation markers. On the other hand, miR-29a and miR-29b targeted MCL1 in the GBM neurospheres and increased apoptotic cell death. Gene expression in differentiated cells relative to neurospheres in four different glioblastoma cultures

2013-03-05 | E-GEOD-44841 | biostudies-arrayexpress

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