Comment[ArrayExpressAccession] E-GEOD-53987 MAGE-TAB Version 1.1 Public Release Date 2014-01-11 Investigation Title Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control Comment[Submitted Name] Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control Experiment Description Schizophrenia is a complex psychiatric disorder encompassing a range of symptoms and etiology dependent upon the interaction of genetic and environmental factors. Several risk genes, such as DISC1, have been associated with schizophrenia as well as bipolar disorder (BPD) and major depressive disorder (MDD), consistent with the hypothesis that a shared genetic architecture could contribute to divergent clinical syndromes. The present study compared gene expression profiles across three brain regions in post-mortem tissue from matched subjects with schizophrenia, BPD or MDD and unaffected controls. Post-mortem brain tissue was collected from control subjects and well-matched subjects with schizophrenia, BPD, and MDD (n=19 from each group). RNA was isolated from hippocampus, Brodmann Area 46, and associative striatum and hybridized to U133_Plus2 Affymetrix chips. Data were normalized by RMA, subjected to pairwise comparison followed by Benjamini and Hochberg False Discovery Rate correction (FDR). Samples derived from patients with schizophrenia exhibited many more changes in gene expression across all brain regions than observed in BPD or MDD. Several genes showed changes in both schizophrenia and BPD, though the magnitude of change was usually larger in schizophrenia. Several genes that have variants associated with schizophrenia were found to have altered expression in multiple regions of brains from subjects with schizophrenia. Continued evaluation of circuit-level alterations in gene expression and gene-network relationships may further our understanding of how genetic variants may be influencing biological processes to contribute to psychiatric disease. Pre-frontal cortex, striatum and hippocampus were obtained from subjects with schizophrenia, bipolar disorder, major depressive disorder and matched controls. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Lanz Lanz Person First Name Thomas Thomas Person Mid Initials A A Person Email thomas.a.lanz@pfizer.com Person Affiliation Pfizer Person Phone 860-686-0546 Person Address Neuroscience, Pfizer, Eastern Point Rd MS# 8220-4243, Groton, CT, USA Person Roles submitter Protocol Name P-GSE53987-1 P-GSE53987-3 P-GSE53987-4 P-GSE53987-2 P-GSE53987-5 Protocol Description R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values. Brain regions were normalized separately. ID_REF = VALUE = RMA expression values Biotinylated cRNA were prepared according to the standard Affymetrix protocol. Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133_Plus 2 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station. Trizol extraction of total RNA was performed. Gene chips were scanned using an Affymetrix 3000 array scanner. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name PMI PH SEX AGE RIN DISEASE STATE RACE ORGANISM PART Experimental Factor Type pmi ph sex age rin disease state race organism part Comment[SecondaryAccession] GSE53987 Comment[GEOReleaseDate] 2014-01-11 Comment[ArrayExpressSubmissionDate] 2014-01-10 Comment[GEOLastUpdateDate] 2014-01-12 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-53987.sdrf.txt