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Systematic meta-analysis and replication of genome-wide expression studies of Parkinson’s disease: 4

ABSTRACT: Analysis of substantia nigra from postmortem brains of 4 patients with Parkinson’s disease (PD). Results provide insight into the molecular processes perturbed in the PD substantia nigra.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20314 | GEO | 2011/01/20

SECONDARY ACCESSION(S): PRJNA129845

REPOSITORIES: GEO

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Systematic meta-analysis and replication of genome-wide expression studies identifies molecular pathways of Parkinson’s disease

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Project description:Analysis of substantia nigra from postmortem brains of 4 patients with Parkinson’s disease (PD). Results provide insight into the molecular processes perturbed in the PD substantia nigra. Fresh frozen tissue blocks from cerebellar hemispheres of PD patients and controls were provided by the Queens Square Brain Bank for Neurological Disorders (London, UK). Total RNA was isolated from about 500 mg fresh frozen postmortem tissue from each subject by using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol and further purified using the RNeasy mini kit (Qiagen, Hilden, Germany). Quality of the extracted total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Cerebellar mRNA with the following criteria: two distinct visible peaks for 18 s and 20 s RNA with lack of multiple small peaks indicating major degradation in Agilent Bioanalyzer fluorograms and GAPDH 3′/5′ ratios smaller 5.0 and percentage present calls greater 40% for the parameter assessed by chip hybridization were hybridized on Affymetrix human U133A GeneChip Array. Sample labeling, hybridization to arrays and image scanning (Affymetrix® GeneChip® Scanner 2500, Agilent technologies, Boblingen, Germany) were performed using standard Affymetrix® protocol (Affymetrix® Expression Analysis Technical Manual) as described previously (Bonin et al, Brain Res. Mol. Brain Res. 126, 2004). The Affymetrix .CEL files were normalized to “all probe sets” in a standardized matter, and scaled to 100 by the MAS5 algorithm implemented in the Bioconductor package.

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