Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 118
Release date: Jan 29 2011
Last update date: Aug 19 2014
Access: Public
Diseases: Alzheimer Disease, Amyotrophic Lateral Sclerosis, Huntington Disease, Multiple Sclerosis, Parkinson Disease, Protein Deficiency, Neurodegenerative Diseases
Chemicals: Somatostatin, Glutamic Acid
Dataset link Common neuroinflammatory pathways in neurodegenerative diseases.

Experimental Protocol


A total of 113 cases were selected retrospectively on the basis of a confirmed clinical and neuropathological diagnosis and snap-frozen brain blocks were provided by various tissue banks within the BrainNet Europe network. Total RNA was extracted from dissected snap-frozen tissue (< 100 mg) by the individual laboratories according to a BNE optimised common protocol using the RNeasy(r) tissue lipid mini kit (Qiagen Ltd, Crawley, UK) according to the manufacturer's instructions, and was stored at -80C until further use. Gene expression analysis was performed on the RNA samples using the Illumina whole genome HumanRef8 v2 BeadChip (Illumina, London, UK). All the labelling and hybridisation of the samples was carried out in a single experiment by the Imperial College group to reduce the technical variability. RNA samples were prepared for array analysis using the Illumina TotalPrep(tm)-96 RNA Amplification Kit (Ambion/Applied Biosystems, Warrington, UK). Finally, the BeadChips we re scanned using the Illumina BeadArray Reader. The data was extracted using BeadStudio 3.2 (Illumina). Data normalisation and gene differential expression analyses were conducted using the Rosetta error models available in the Rosetta Resolver(r) system (Rosetta Biosoftware, Seattle, Wa, USA). Two samples presented very low signal expression most likely due to hybridization problems and did not pass the quality control test. They are not represented here. One of the 2 samples was a replicate, therefore there was loss of only 1 case bringing the grand total of cases used to 112 (total of samples of 118 including 6 replicates).

Repositories


GEO

GSE26927

ArrayExpress

E-GEOD-26927

BioProject

PRJNA136075

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Contact


Pascal Durrenberger
Pascal Francis Durrenberger