Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA135681 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-SEQ profiling of dopaminergic neurons from the substantia nigra pars compacta and ventral tegmental area regions of the mouse mid-brain Murine midbrain dopaminergic neurons from the SNpc and VTA regions
2015-07-27 | E-GEOD-64452 | biostudies-arrayexpress
Project description:Directed differentiation of midbrain dopaminergic neurons from human embryonic stem cells (hESCs) has galvanized much interest into their potential application in human Parkinson’s disease (PD). We conducted genome-wide, exon-specific expression analyses at three temporally and phenotypically distinct stages of lineage restriction (pluripotent hESCs, multipotent neural precursor cells and terminally differentiated midbrain dopaminergic neurons). We compare these to expression data generated on the same platform from samples isolated from human fetal brain and from human control postmortem samples isolated from the substantia nigra. This comparison highlights the commonalities and differences between neural cells derived from hESCs and their counterparts in the human brain. This gene expression microarray study was carried out to i) identify changes in gene expression and splicing during neural differentiation to dopaminergic neurons, and ii) determine the maturational state of hESC-derived neuronal samples particularly with regard to genes and pathways relevant to Parkinson's disease.
2014-12-01 | GSE34865 | GEO
Project description:RNA-SEQ profiling of dopaminergic neurons from the substantia nigra pars compacta and ventral tegmental area regions of the mouse mid-brain
2015-07-27 | GSE64452 | GEO
Project description:The cardinal clinical features of Parkinson's disease result from selective loss of midbrain dopaminergic neurons. The goal of this experiment is to determine the gene expression profiles of these neurons by studying untreated rat substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopaminergic neurons using laser capture microscopy to obtain region-specific neuronal mRNA.
2007-10-27 | E-GEOD-1157 | biostudies-arrayexpress
Project description:Our goal was to develop a list of genes that could be used effectively to highlight the genomic profiling of human embryonic neural stem cells (hENSCs), and to identify genes involved in the process of their differentiation to dopaminergic (DA) neurons. Our results showed that Agilent's Whole Human Genome Oligonucleotide Microarray permits the monitoring of at least 41000 genes as cells differentiate. In this study, we identified 13525 genes to be differentially expressed between undifferentiated hENSC and DA cells isolated from human substansia nigra. Approximately 3737 genes were up-regulated in the embryonic NSC, and 4116 genes were up-regulated in DA cells. Careful analysis of the emerged data using the web-accessible program named Database for Annotation, Visualization and Integrated Discovery (DAVID) has permitted us to distinguish several genes and pathways that are involved in dopaminergic differentiation, and to identify the crucial signaling pathways that direct the process of differentiation. Our study elucidated that genes related to midbrain development, such as Nr4a2 (nuclear receptor subfamily 4, group A, member 2, Nurr1) and En1 (engrailed 1), were increased to 3.76- and 6.41-folds, respectively. In addition, the transcriptions of the genes for DA neuron phenotype, such as Ddc (doapmine decarboxylase, AADC), Slc6a3 (solute carrier family 6, member 3, DAT), and Th (tyrosine hydroxylase), were significantly increased to 8.08, 4.01, and 5.91, respectively. As data accumulate with different populations and different methods of differentiation, one will perhaps be able to identify the key regulators and biomarkers that may allow selective selection of limited number of genes or transcription factors to be used for direct reprogramming of NSC into DA cells, with an ultimate goal of obtaining different types of allogenic neurons including personalized DA neurons to be used in replacement therapy for neurodegenerative diseases such as Parkinson's disease (PD). Two-condition experiment: hENSC S vs. DA cells. Biological replicates: 2 hENSC, and 2 DA neuron samples from human substantia nigra cells.
2011-10-26 | E-GEOD-25931 | biostudies-arrayexpress
Project description:Recent advances in three dimensional (3D) culture systems have led to the generation of brain organoids that share resemblance to different parts of the human brains; however, a 3D organoid model of the midbrain that contains functional midbrain dopaminergic (mDA) neurons has not been reported. In this study, we develop a method to differentiate human PSCs into a large multicellular organoid-like structure that contains distinct layers of neuronal cells with a transcriptomic profile that resembles human prenatal midbrain. Importantly, we detected electrically active and functionally mature mDA neurons, and dopamine production in our 3D midbrain-like organoids (MLOs). In contrast to human mDA neurons generated using non-3D methods or in the MLOs generated from mouse embryonic stem cells, our human MLOs uniquely produced neuromelanin-like granules that were structurally similar to those isolated from human substantia nigra tissues. Thus our MLOs bearing features of the human midbrain may provide a novel tractable in vitro system to study the human midbrain and its related diseases.
2016-08-24 | E-MTAB-4868 | biostudies-arrayexpress
Project description:Engrailed homeoproteins are expressed in adult dopaminergic neurons of the substantia nigra. In Engrailed1 heterozygous mice, these neurons start dying at 6 weeks, are more sensitive to oxidative stress and progressively develop traits similar to those observed following an acute and strong oxidative stress inflected to wild-type neurons. These changes include DNA strand breaks and the modification (intensity and distribution) of several nuclear and nucleolar heterochromatin marks. Engrailed1 and Engrailed2 are biochemically equivalent transducing proteins previously used to antagonize dopaminergic neuron death in Engrailed heterozygous mice and in mouse models of Parkinson disease. Accordingly, we show that, following an acute oxidative stress, a single Engrailed2 injection restores all nuclear and nucleolar heterochromatin marks, decreases the number of DNA strand breaks and protects dopaminergic neurons against apoptosis. RNA-seq data for differentially expressed genes in the SNpc of En1+/- mice, En2 infused mice and 6-OHDA/En2 injection experiments.
2015-09-24 | E-GEOD-72321 | biostudies-arrayexpress
Project description:Parkinson's disease (PD) is a progressive neurodegenerative disorder, which is characterised by degeneration of distinct neuronal populations, including dopaminergic neurons of the substantia nigra. Here, we use a metabolomics profiling approach to identify changes to lipids in PD observed in sebum, a non-invasively available biofluid. We used liquid chromatography-mass spectrometry (LC-MS) to analyse 274 samples from participants (80 drug naïve PD, 138 medicated PD and 56 well matched control subjects) and detected metabolites that could predict PD phenotype. Pathway enrichment analysis shows alterations in lipid metabolism related to the carnitine shuttle, sphingolipid metabolism, arachidonic acid metabolism and fatty acid biosynthesis. This study shows sebum can be used to identify potential biomarkers for PD.
2020-12-21 | MTBLS2266 | MetaboLights
Project description:The cardinal clinical features of Parkinson's disease result from selective loss of midbrain dopaminergic neurons. The goal of this experiment is to determine the gene expression profiles of these neurons by studying untreated rat substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopaminergic neurons using laser capture microscopy to obtain region-specific neuronal mRNA. WARNING: These data are identical to those represented in GEO Series GSE1837.
2004-03-29 | GSE1157 | GEO
Project description:Parkinson's disease (PD) is the second most common neurodegenerative disease, involving the selecive death of dopaminergic neurons in the substantia nigra pars compacta brain region. Here, we performed next generation sequencing on RNA extracted from human substantia nigra tissue. The samples, acquired from the Netherland's Brain Bank, were taken post-mortem from PD and non-PD control donors. Analysis of the data revealed an upregulation of lncRNA LINC-PINT in PD substantia nigra. LINC-PINT interracts with the Polycomb Repressive Complex 2 (PRC2), inhibiting the tracription of multiple targets. Correspondingly, analysis of the data revealed that targets of PRC2 displayed larger disease-associated differences as compared to other genes, as well as enrichment for downregulation, suggesting that the differential expression of LINC-PINT in PD effects LINC-PINT/PRC2 interaction as well.
2020-04-14 | GSE114517 | GEO