GEO DataSets

(Submitter supplied) Aging and its physiological manifestations have been correlated with adult stem cell exhaustion and a failure to maintain tissue homeostasis1-10. Since multiple morphological cellular defects are associated with aging-related disorders, we hypothesized that late onset disorders might be linked to adult stem cell abnormalities compromising cellular function over time. Our work shows that a dominant G2019S mutation in the human LRRK2 gene, which is associated with central nervous system disorders, including Parkinson’s disease, the second most prevalent neurodegenerative disease in the aging population, causes alterations in neural stem cell homeostasis in aging-related cellular contexts. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: BED, BW

(Submitter supplied) Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population. In this study, we generated H9 hESC harboring LRRK2 (G2019S) mutation by gene knockin. Wildtype and LRRK2 mutant hESC were differentiated into NSC using a chemically defined protocol.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4401

Platform:

GPL571

9 Samples

Download data: CEL

(Submitter supplied) Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population. In this study, we generated human induced pluripotent stem cell (iPSC) lines from LRRK2 (G2019S) bearing patient fibroblasts by cell reprogramming. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4400

Platform:

GPL571

14 Samples

Download data: CEL

Analysis of LRRK2 (Gly2019Ser) mutant neural stem cells (NSC) treated with LRRK2 kinase specific inhibitor LRRK2-IN-1. The LRRK2 (G2019S) mutation causes familial Parkinson's disease. Results provide insight into molecular basis of progressive degeneration of NSCs caused by pathogenic LRRK2.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 agent, 2 genotype/variation sets

Platform:

GPL571

Series:

GSE36321

9 Samples

Download data: CEL

Analysis of IPSCs generated from LRRK2 (Gly2019Ser) mutation-bearing patient fibroblasts by cell reprogramming. The LRRK2 (G2019S) mutation causes familial Parkinson's disease (PD). Results provide insight into the molecular mechanisms underlying PD.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 cell type, 3 genotype/variation sets

Platform:

GPL571

Series:

GSE33298

14 Samples

Download data: CEL

(Submitter supplied) We have generated isogenic induced pluripotent stem cell lines by reprogramming human fibroblasts from patients carrying the LRRK2 G2019S mutation with subsequent zinc finger nuclease - mediated targeted correction of the diseased allele. These iPS cell lines were differentiated for 30 days using a direct differentiation protocol towards midbrain dopaminergic neurons (mDANs).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) Analysis of whole genome expression in control and patients with Parkinsons disease iPSC lines. The hypothesis tested in present study was that deficient GBA, SNCA, LRRK2 and PARKIN expression can be used for disease modeling by their affects on multiple pathways. These results provide information on relationship between PD genes and mitochondria related gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) Emerging evidence suggest that Parkinson's disease (PD), besides being an age-associated disorder, might also have a neurodevelopment component. Disruption of mitochondrial homeostasis has been highlighted as a crucial cofactor in its etiology. Here, we show that PD patient-specific human neuroepithelial stem cells (NESCs) carrying the LRRK2-G2019S mutation recapitulate key mitochondrial defects previously described only in differentiated dopaminergic neurons. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: TXT

(Submitter supplied) Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson’s disease (PD), dopaminergic neurons are a vulnerable population progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains mostly unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

27 Samples

Download data: XLSX

(Submitter supplied) Non-neuronal cell types such as astrocytes can contribute to Parkinson’s disease (PD) pathology. The G2019S mutation in leucine-rich repeat kinase 2 (LRRK2) is one of the most common known causes of familial PD. To characterize its effect on astrocytes, we developed a protocol to produce midbrain-patterned astrocytes from human induced pluripotent stem cells (iPSCs) derived from PD LRRK2 G2019S patients and healthy controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL5175

42 Samples

Download data: CEL

(Submitter supplied) We analysed the RNA profile of IPSC-derived dopaminergic neurons from idiophatic and genetic form (LRRK2) of Parkinson’s disease (PD). Both, idiopathic and genetic form of the disease show similar expression alterations and were merged in one whole PD group. We found 437 differentially expressed genes (DEGs) in the PD group as a whole. Up-regulated DEGs (n=254) encompassed genes involved in neural functions and transcription factor functions whereas down-regulated DEGs (n=183) affected basic homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

14 Samples

Download data: CEL

(Submitter supplied) We performed a genome-wide DNA methylation study in induced pluripotent stem cells (IPSC)-derived dopaminergic neurons (DAn) generated from keratinocytes of monogenic and sporadic Parkinson disease (PD) patients as well as of healthy subjects. We observed extensive DNA methylation changes in DAn from PD patients. These changes were neither present in the original keratinocytes nor in the undifferentiated IPSCs, suggesting latent molecular defects in PD keratinocytes that are manifested only upon differentiation into DAn. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

28 Samples

Download data: TXT

(Submitter supplied) This submission contains a result of a study of transcriptiomic profiles of the IPSC and NPC, derived from PD discordant monozygous twins.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

24 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15433

201 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing of small RNAs (mature miRNA and piRNA/piRNA-like molecules) from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=26) and differentiated midbrain neurons (n=10). In parallel, cingulate gyrus samples from eight control- and eight Parkinson´s disease patients obtained from the Netherlands Brain Bank were sequenced. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15433

69 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing of MSPI digested, size selected and bisulfite converted genomic DNA from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=26) and differentiated midbrain neurons (n=10). We were able to sequence more than 400,000 CpGs at ≥5x coverage in all samples. Nonetheless, statistical analysis with RnBeads did not identify major differences on single CpG or promoter methylation level between control- and Parkinson´s disease patient derived cells in any cell type.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15433

53 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing of poly-A RNA from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=31) and differentiated midbrain neurons (n=15). Fibroblasts and iPSCs do not show major differences on single gene level. In contrast, midbrain neurons derived from Parkinson´s disease patients show changes known to be associated with neurodegenerative diseases.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

63 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing of coding exome RNA from cingylate gyrus brain tissue obtained from control- and Parkinson´s disease patients. In the Parkinson´s disease affected tissue, changes are present that are known to be related to the pathogenesis of neurodegenerative diseases.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

16 Samples

Download data: TXT