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Gene expression profiling of substantia nigra: a post-mortem study in Parkinson's disease and control subjects

ABSTRACT: Gene expression profiling of substantia nigra: a post-mortem study in Parkinson's disease and control subjects

PROVIDER: PRJEB65876 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12020761_1.fastq.gz	Fastqsanger.gz
	ERR12020761_2.fastq.gz	Fastqsanger.gz
	ERR12020762_1.fastq.gz	Fastqsanger.gz
	ERR12020762_2.fastq.gz	Fastqsanger.gz
	ERR12020763_1.fastq.gz	Fastqsanger.gz

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Gene expression profiling of substantia nigra: a post-mortem study in Parkinson's disease and control subjects

Project description:Introduction: Parkinson's disease (PD) is characterized by bradykinesia, tremor, and rigidity; in addition, postural instability sets in as the disease progresses. Non-motor symptoms of the disease include cognitive, behavioral, and neuropsychiatric changes, sensory and sleep disturbances that may precede the motor symptoms of the disease itself. The peculiar pathological features of PD are decreased dopaminergic neurons and dopamine levels in the substantia nigra pars compacta and pontine locus ceruleus. The study of the transcriptome plays a major role in the identification of genes and gene regulatory mechanisms in multifactorial neurodegenerative diseases such as Parkinson's disease itself. Therefore, we proposed to study the transcriptome directly in the midbrain containing the "Substantia nigra.The study was performed in 8 subjects with PD and 6 normal control subjects, using next-generation sequencing (NGS) technologies. Results: With the use of an ad hoc bioinformatics pipeline, gene expression profiles in the different PD subjects were obtained and compared to those of controls. In detail, the results obtained from the data analysis indicated 92 differentially expressed genes (FDR-adjusted p value ≤0.05 and fold-change less than -1.5 or greater than +1.5) of which 33 genes were up-regulated while 59 were down-regulated. Conclusions: Functional analysis of the differentially expressed genes revealed several genes involved in different canonical pathways indicating their likely significant role in Parkinson's disease.

2024-01-03 | E-MTAB-13295 | biostudies-arrayexpress

Next generation sequencing reveals upregulation of the lncRNA LINC-PINT in the substantia nigra of human Parkinson's disease patients compared to control donors

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

Transcriptome-wide changes in the Substantia Nigra following Deep Brain Stimulation in the Subthalamic Nuecleus of a PD rat model.

Project description:In this study we identify the gene espression changes that occur in the substantia nigra in a Parkinson's Disease (PD) rat model with and without deep brain stimulation (DBS). A rat model of PD was created as previously described by stereotacticaly injecting an AAV-expressing the human A53T_mutated form of a-Synuclein into the Substantia Nigra of adult rats, while control rats were injected with empty vector (EV). These mice exhibit neurodegeneration in the Substantia Nigra and Parkinson-like behaviour phenotypes. Sixteen weeks after the injection, RNA was isolated from the Substantia Nigra and Striatum. Single-end 75nt high throughput sequencing were performed on libraries prepared from the RNA. We identified over 200 genes that were differentially expressed between control and Parkinson's ratswith a log2 fold-change > |0.6|. These genes were enriched for terms related to immune activation. The genes associated with these GO terms tended to be up-regulated in the Parkinson's rats suggesting that brain-localized immune cells are more activated in Parkinson's disease. Interestingly in the rats treated with DBS, these immune-related genes were comparable to control animals.

2024-12-09 | GSE263579 | GEO

Age-mediated transcriptomic changes in adult mouse substantia nigra

Project description:Substantia nigra pars compacta (SNpc) is highly sensitive to normal aging and selectively degenerates in Parkinson's disease. Until now, molecular mechanisms behind SNpc aging have not been fully investigated using high throughput techniques. Here, aging-associated early changes in transcriptome of SNpc were investigated comparing late middle-aged (18 months old) to young (2 months old) mice.

2013-05-29 | GSE45043 | GEO

Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease

Project description:Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease

| PRJNA767088 | ENA

Transcriptional interaction network analyses in dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra in Parkinson's disease

Project description:We analyzed the transcriptomic profile of post-mortem explants from dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra obtained from controls and Braak 4 (BK4) and 5 (BK5) stages of Parkinson’s disease (PD) patients in order to investigate how gene-gene interaction patterns vary along different anatomical regions in patients and controls. The comparative transcriptional networks analyses indicate that the main hubs in PD networks are related to ubquitin/proteasome, oxidative stress, neuroprotection, neurogenesis and PD associated proteins.

2015-01-11 | GSE43490 | GEO

Transcription profiling of human substantia nigra from postmortem brain of Parkinsons disease patients (PD)

Project description:We used microarrays to detail the global program of gene expression underlying Parkinson's disease Experiment Overall Design: Substantia nigra tissue from postmortem brain of normal and Parkinson disease patients were used for RNA extraction and hybridization on Affymetrix microarrays: 9 replicates for the controls and 16 replicates for the Parkinson's disease patients were used. Both cohorts included males and females.

2008-11-06 | E-GEOD-7621 | biostudies-arrayexpress

Transcriptional analysis of whole substantia nigra in Parkinson's disease

Project description:Post mortem tissue was dissected from two groups of age and gender matched groups of Parkinson and Control subjects

2010-03-12 | GSE20292 | GEO

Transcriptomic profiling of substantia nigra and putamen in Parkinson’s disease

Project description:We report RNA sequencing results of human substantia nigra and putamen samples from Parkinson's disease patients and controls. Each substantia nigra sample is the result of pooling brain tissue from two individuals with the same , while each putamen sample is the result of pooling brain tissue from three individuals. We found 354 differentially expressed genes (DEGs) in the SN of PD patients compared to age-matched controls, while we observed 261 DEGs in the putamen samples. The top-enriched pathways from the SN were associated with “protein folding” and “neurotransmitter transport”, and the putamen DEGs with “synapse organization”. In summary, our data confirms the key role of protein folding and neuronal degeneration in the pathology of PD, and highlights new genes and pathways that have not yet been explored in the context of PD.

2020-09-02 | GSE136666 | GEO

Transcription profiling of human Parkinsons medial and substania nigra

Project description:Affymetrix HG_U133 array sets (A and B chips) were used to determine the whole genome transcription profile of clinically documented and neuropathologically confirmed cases of sporadic Parkinson's disease as well as controls. Experiment Overall Design: Post mortem brain tissue samples from Parkinson's disease and control cases (substantia nigra, split into medial and lateral portions, and frontal cortex) were prepared for this study. In total, 47 individual tissue samples were analyzed using one A and one B GeneChip per sample, i.e. 15 samples of medial parkinsonian SN, 9 samples of lateral parkinsonian SN, 8 medial nigra control samples and 7 lateral nigra control samples. Lateral and medial nigra samples were from the same cases. In addition, frontal cerebral cortex was analyzed in five of the PD cases and in three of the controls (Neurogenetics 2006 7: 1â??11; Acta Neuropathologica (Berlin) 2007 113: 253-263

2008-06-16 | E-GEOD-8397 | biostudies-arrayexpress

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