E-MTAB-9045
Ontology highlight
ABSTRACT:
DISEASE(S): Normal,Cornelia De Lange Syndrome
PROVIDER: E-MTAB-9045 | ExpressionAtlas | 2020-07-20
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as RNA originating from enhancer transcription. We characterised promoter-level gene expression in cortical neurons from CdLS patients and found deregulation of hundreds of genes enriched for neuronal functions.
2021-02-27 | E-MTAB-9045 | biostudies-arrayexpress
Project description:Nuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals
| PRJEB38243 | ENA
Project description:Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Cav1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca2+) signaling and activity-dependent gene expression and show abnormalities in differentiation. Neurons from individuals with Timothy syndrome show increased expression of markers of the upper cortical layer and decreased expression of callosal projection markers. In addition, the mutation that causes Timothy syndrome leads to an increase in the production of neurons that synthesize norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase and atypical L-type–channel blocker. These findings provide strong evidence that Cav1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome. Total RNA was isolated from control and TS cells: fibroblasts, iPSCs, neurospheres (at day 7 in suspension), neurons at rest (day 45 of differentiation) and neurons kept in 67mM KCl for 9h. For sample titles, D1,D2 and D3 represent independent differentiation experiments. The number after - represents the iPSC cell line number. GSE25542_non-normalized.txt.gz contains data for 5 outliers.
2011-11-07 | E-GEOD-25542 | biostudies-arrayexpress
Project description:Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Cav1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca2+) signaling and activity-dependent gene expression and show abnormalities in differentiation. Neurons from individuals with Timothy syndrome show increased expression of markers of the upper cortical layer and decreased expression of callosal projection markers. In addition, the mutation that causes Timothy syndrome leads to an increase in the production of neurons that synthesize norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase and atypical L-type–channel blocker. These findings provide strong evidence that Cav1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome.
2011-11-07 | GSE25542 | GEO
Project description:It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA-rearrangements in the human neocortex. We show here that neither is the case, using immunohistochemistry, transcriptome-, genome- and ploidy-analyses, and determination of nuclear bomb test-derived 14C-concentration in neuronal DNA. A large proportion of cortical neurons display DNA-fragmentation and DNA-repair short time after stroke, whereas neurons at chronic stages after stroke show DNA-integrity, demonstrating the relevance of an intact genome for survival. Analyze of potential fusion transcripts in 13 samples, seven cortical ischemic stroke tissue and six control cortex, by deep sequencing using Illumina HiSeq 2000
2014-03-28 | E-GEOD-56267 | biostudies-arrayexpress
Project description:To understand how NSD1 inactivation deregulates transcription, and to explore how this transcriptional deregulation affect human development, we profiled transcription in Sotos syndrome patients and healthy control individuals.
2022-03-01 | GSE191274 | GEO
Project description:Layer II stellate neurons (entorhinal cortex) and layer III cortical neurons (hippocampus CA1, middle temporal gyrus, posterior cingulate, superior frontal gyrus, primary visual cortex) were gene expression profiled. Brain regions are from individuals who had been diagnosed with mild cognitive impairment. Experiment Overall Design: ~500 neurons were selected from each of 6 brain regions. Total RNA was isolated from each batch of neurons, double round amplified, and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays.
2009-09-05 | E-GEOD-9770 | biostudies-arrayexpress
Project description:Down syndrome (trisomy 21) is the most common genetic cause of intellectual disability, but the precise molecular mechanisms underlying impaired cognition remain unclear. Elucidation of these mechanisms has been hindered by the lack of a model system that contains full trisomy of chromosome 21 (Ts21) in a human genome that enables normal gene regulation. To overcome this limitation,we created Ts21-induced pluripotent stem cells (iPSCs) from two sets of Ts21 human fibroblasts. One of the fibroblast lines had low level mosaicism for Ts21 and yielded Ts21 iPSCs and an isogenic control that is disomic for human chromosome 21 (HSA21). Differentiation of all Ts21 iPSCs yielded similar numbers of neurons expressingmarkers characteristic of dorsal forebrain neurons that were functionally similar to controls. Expression profiling of Ts21 iPSCs and their neuronal derivatives revealed changes in HSA21 genes consistent with the presence of 50% more genetic material as well as changes in non- HSA21 genes that suggested compensatory responses to oxidative stress. Ts21 neurons displayed reduced synaptic activity, affecting excitatory and inhibitory synapses equally. Thus, Ts21 iPSCs and neurons display unique developmental defects that are consistent with cognitive deficits in individuals with Down syndrome and may enable discovery of the underlying causes of and treatments for this disorder. Three independent RNA samples were collected from Down syndrome (DS) and control iPSCs between passages 24 and 48. Three independent RNA samples were collected from 30 day old neurons differentiated from Down syndrome (DS) and control iPSCs.
2013-07-09 | E-GEOD-48611 | biostudies-arrayexpress
Project description:Gene expression from icas9 human iPSC derived cortical neurons treated with and without doxycycline
| EGAS00001004782 | EGA
Project description:Limited data exists on alterations in DNA methylation that are associated with Autosomal Dominant Polycystic Kidney Disease (ADPKD). Given there are similarities between cystic kidney disease and neoplasia, and that DNA methylation inhibitors are FDA-approved for the treatment of myelodysplastic syndrome, we performed genome-scale methylation analysis of cortical kidney tissue from four ADPKD patients and nonADPKD cortical kidney tissue from three individuals to identify the methylation patterns of ADPKD tissue.
2019-12-01 | GSE110057 | GEO