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E-GEOD-20314 - Systematic meta-analysis and replication of genome-wide expression studies of Parkinson’s disease: 4

Status
Released on 20 January 2011, last updated on 27 March 2012
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (6)
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.
Experiment type
transcription profiling by array 
Contacts
Bin Zheng, Clemens R Scherzer, Ullrich Wüllner
Citation
PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. Zheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, Eklund AC, Zhang-James Y, Kim PD, Hauser MA, Grünblatt E, Moran LB, Mandel SA, Riederer P, Miller RM, Federoff HJ, Wüllner U, Papapetropoulos S, Youdim MB, Cantuti-Castelvetri I, Young AB, Vance JM, Davis RL, Hedreen JC, Adler CH, Beach TG, Graeber MB, Middleton FA, Rochet JC, Scherzer CR, Global PD Gene Expression (GPEX) Consortium. , PMID:20926834
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20314.idf.txt
Sample and data relationshipE-GEOD-20314.sdrf.txt
Raw data (1)E-GEOD-20314.raw.1.zip
Processed data (1)E-GEOD-20314.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-20314.eSet.r
Links