{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["William Davies"],"study_type":["transcription profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16677"],"description":["Peripheral regulatory T-cell (Treg) levels correlate with psychiatric outcomes in humans, and Treg-depletion induced by diptheria toxin administration in Foxp3DTR knock-in mice results in specific behaviour phenotypes.   We examined the consequences of Treg depletion on whole brain gene expression in adult female mice through comparing Foxp3DTR mice administered either diptheria toxin (causing depletion, three biological replicates) or vehicle solution (resulting in Treg persistence, three biological replicates)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Biotin-labelled targets for the microarray experiment were prepared using 100ng of total RNA per replicate. Sense single-stranded cDNA was synthesized, fragmented and labelled using the Genechip WT PLUS Reagent Kit (Affymetrix) in conjunction with the Affymetrix Genechip Poly-A RNA Control Kit as described in the User Manual (P/N 703174).","Scaning - The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) in conjunction with Affymetrix Genechip Command Console (AGCC) software.","Hybridization - A hybridization cocktail containing the biotinylated target was incubated with the GeneChip Mouse 2.0 ST array (Affymetrix) at 60rpm for 16hr at 45°C in a Genechip Hybridisation Oven 645. After hybridization, non-specifically bound material was removed by washing, and specifically-bound target was detected using the GeneChip Hybridization, Wash and Stain Kit, in conjunction with the GeneChip Fluidics Station 450 (Affymetrix).","Sample Treatment - Mice were injected with diphtheria toxin or PBS vehicle intraperitoneally on Days 1 and 3 to induce Treg depletion, and culled 24hrs after the final injection","Sample Collection - Whole brain extracted from adult female mice culled by cervical dislocation, bisected sagitally, and flash-frozen at -80C. Right hemisphere used for microarray analysis.","Nucleic Acid Extraction - High-quality total RNA extracted from individual hemibrains using RNeasy Plus Universal Midi Kit (Qiagen) according to the manufacturer’s instructions. Three biological replicates per group were generated, with each replicate containing equal amounts of RNA pooled from 3-5 brains; 260/280 absorbance ratios of 2.06-2.09 and RIN numbers of 9.3-9.5 were recorded for the six replicates using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["William Davies"],"data_protocol":["Data Transformation - Data were normalised using Robust Multiarray Average (RMA); the overall pattern of normalised expression data appeared equivalent across the six replicates."],"additional_accession":[]},"is_claimable":false,"name":"Microarray of whole brain gene expression in transgenic adult female mice expressing primate diphtheria toxin receptor under Foxp3 promoter (Foxp3DTR) treated with either diphtheria toxin or vehicle","description":"Peripheral regulatory T-cell (Treg) levels correlate with psychiatric outcomes in humans, and Treg-depletion induced by diptheria toxin administration in Foxp3DTR knock-in mice results in specific behaviour phenotypes.   We examined the consequences of Treg depletion on whole brain gene expression in adult female mice through comparing Foxp3DTR mice administered either diptheria toxin (causing depletion, three biological replicates) or vehicle solution (resulting in Treg persistence, three biological replicates).","dates":{"release":"2026-07-01T00:00:00Z","modification":"2026-07-01T01:04:18.053Z","creation":"2026-02-25T00:57:22.438Z"},"accession":"E-MTAB-16677","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815","EFO_0003969"]}}