Comment[ArrayExpressAccession] E-GEOD-48954 MAGE-TAB Version 1.1 Public Release Date 2013-07-18 Investigation Title Psychotropic drug-induced gene expression alterations in mouse striatum II Comment[Submitted Name] Psychotropic drug-induced gene expression alterations in mouse striatum II Experiment Description To identify the molecular mechanisms that may initiate therapeutic effects, whole-genome expression profiling (Illumina Mouse WG-6 microarrays) of drug-induced alterations in the mouse brain was undertaken, with a focus on the time-course (1, 2, 4 and 8h) of gene expression changes produced by eighteen major psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. The resulting database is freely accessible at www.genes2mind.org. Bioinformatics approaches led to the identification of three main drug-responsive genomic networks and indicated neurobiological pathways that mediate the alterations in transcription. Each tested psychotropic drug was characterized by a unique gene network expression profile related to its neuropharmacological properties. Functional links that connect expression of the networks to the development of neuronal adaptations (MAPK signaling pathway), control of brain metabolism (adipocytokine pathway), and organization of cell projections (mTOR pathway) were found. The additional data-sets are available at GEOX1 and GEOX2. The microarray experiment was performed to analyze time-course of drug-induced transcriptional response in C57BL/6J mouse striatum. Three antidepressants (bupropion 20 mg/kg, tranylcypromine 20 mg/kg, mianserin 20 mg/kg, i.p.), three anxiolytics (diazepam 5 mg/kg, buspirone 10 mg/kg, hydroxyzine 10 mg/kg, i.p.), and three antipsychotics (clozapine 3 mg/kg, risperidone 0.5 mg/kg, haloperidol 1 mg/kg) were selected for the comparison. Drug doses were previously reported as effective in mice and further tested in our laboratory. To analyze dynamics of early, intermediate and relatively late changes of mRNA abundance the experiment was performed in four time points (1, 2, 4 and 8h after drug administration). To exclude influence of drug injection and circadian rhythm on gene expression profile, control groups of saline or tween (1% Tween 80) treated and naïve animals were prepared for each time point. Design of the experiment assumed pooling of two animals per each array and using of three independent arrays per group. To provide appropriate balance in the whole dataset groups were equally divided between the array hybridization batches. 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 Piechota Piechota Korostynski Person First Name Marcin M M Person Email marpiech@if-pan.krakow.pl Person Affiliation Institute of Pharmacology PAS Person Phone (+4812) 6623328 Person Address Molecular Neuropharmacology, Institute of Pharmacology PAS, Smetna 12, Krakow, Poland Person Roles submitter Protocol Name P-GSE48954-1 P-GSE48954-3 P-GSE48954-4 P-GSE48954-2 P-GSE48954-5 Protocol Description The data were normalised using quantile normalisation with preprocessCore in R. ID_REF = VALUE = quantile normalized signal intensity Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. Standard Illumina hybridization protocol. RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Standard Illumina scanning protocol. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name TIME DRUG Experimental Factor Type time drug Comment[SecondaryAccession] GSE48954 Comment[GEOReleaseDate] 2013-07-18 Comment[ArrayExpressSubmissionDate] 2013-07-17 Comment[GEOLastUpdateDate] 2013-07-19 Comment[AEExperimentType] transcription profiling by array Comment[AdditionalFile:Data1] GSE48954_non-normalized.txt SDRF File E-GEOD-48954.sdrf.txt