{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mario Fraga"],"study_type":["methylation profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15631"],"description":["Microglial replacement is emerging as a promising approach for treating age-related disorders, but effects on epigenetic age remain unclear. We examined DNA methylation changes in mouse microglia influenced by age and microglial replacement using Infinium Mouse Methylation BeadChips. We analyzed the FACS-sorted microglia of young (N=4), old (N=4) and old with microglial replacement (N=4) achieved using a PLX diet. Old microglia showed an aged epigenetic profile. Microglial depletion/repopulation, driving proliferation, led to accelerated epigenetic age. However, at the genome-wide level, repopulation reversed many aging-related changes, particularly those linked to immune and inflammatory response."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Labelling was performed automatically during the post-amplification xStain process and is achieved using Biotin and DNP labelled antibodies.","Nucleic Acid Extraction - Genomic DNA was extracted with the phenol-chloroform procedure and quantified with Nanodrop/Qubit.","Scaning - IDAT files were preprocessed with the R/Bioconductor package sesame (v1.20.0) under recommended parameters for mouse arrays (“prep” argument set to “TQCDPB”), which includes non-linear dye bias correction and noob background correction.","Sample Collection - C57BL/6 adult young (3–4 months) mice and old (21–22 months) mice were obtained from Janvier (Lyon, France) or Envigo (Amsterdam, The Netherlands). Mice were maintained at the animal facility at the School of Medicine or Faculty of Psychology of the University of Barcelona (UB) under standardized environmental conditions, a 12 h dark/light cycle, and ad libitum access to food and water. Animal work was conducted following the Catalan and Spanish laws (Real Decreto 53/2013) and the European Directives. All experiments were conducted with the approval of the ethical committee (Comité Ètic d’Experimentació Animal, CEEA) of Universitat de Barcelona, and the local regulatory bodies of the Generalitat de Catalunya, and in compliance with the NIH Guide for the Care and Use of Laboratory Animals.  Mice were anesthetized with isoflurane and euthanized by cervical dislocation. Brains were collected in 50 mL falcon tubes with cold HBSS buffer (w/o Ca2+ and Mg2+; #14175-053, Thermo Fisher Scientific) and placed on ice. The forebrain was dissected with a scalpel, discarding the cerebellum and the olfactory bulbs. The ipsilateral and contralateral hemispheres were separated, minced into small pieces and placed into gentleMACS™ C-Tubes (#130-096-334, Miltenyi Biotec). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit (P) (#130-092-628, Miltenyi Biotec). The gentleMACSTM Octo Dissociator (#130-096-427, Miltenyi Biotec) was used for mechanical dissociation steps following the Neural Tissue Dissociation Kit (P) manufacturer protocol for dissociation with heaters (1× m_Brain_1 program and 1× ABDK_37C program by Miltenyi). The digested tissue was then filtered through a 70 µm cell strainer (#352350, Falcon), previously humidified, with Hanks’ balanced salt solution (HBSS) with Ca2+ and Mg2+ (#14025-092, Thermo Fisher Scientific). Then, cells were separated from myelin by an immunomagnetic separation method. Brain cells were incubated with Myelin Removal Beads II (#130-096-733, Miltenyi Biotec) and then passed through LS Columns (#130-042- 401, Miltenyi Biotec) held onto the OctoMACS Separator (#130-091- 051, Miltenyi Biotec) and to the MACS MultiStand (#130-042-303, Miltenyi Biotec). The negative fraction was collected to continue with the staining protocol. Unspecific binding of antibodies was blocked by previous incubation for 10 min with anti-CD16/CD32 (Fc block, clone 2.4G2; #55314, BD Pharmingen) in Fluorescence-Activated Cell Sorting (FACS) buffer at 4°C. Live/dead Aqua cell stain (#L34957, Thermo Fisher Scientific) was used to determine cell viability. Cells were then incubated with the following primary antibodies during 30 min at 4°C: CD11b (clone M1/70, AF647, #557686, BD Pharmigen), CD45 (clone 30-F11, FITC, #553080, BD Pharmingen) and CD31 (clone 390, PE-Cy7, #25-0311-82, eBioSciences). After washing with FACS Stain Buffer (#554656, BD Biosciences), cells were sorted in a FACS Aria II or FACS Aria SORP sorter (BD Biosciences) using FacsDiva software (version 5, BD Biosciences, San Jose, CA, USA). Microglial cells were collected in sterile 1.5 mL Eppendorf tubes previously coated with FBS (#A3160501, Thermo Fisher Scientific) and 200 µL of cold dPBS (#14190-094, Thermo Fisher Scientific). As fast as possible, cells were centrifuged and resuspended in lysis buffer (from PureLinkTM RNA Micro Kit #12183016, Invitrogen) supplemented with 10% β-mercaptoethanol and finally snap-frozen in dry ice. Data analyses were performed with FlowJo software (version 10, FlowJo LLC, Ashland, OR, USA).","Hybridization - The arrays were scanned with iScan (Illumina) in accordance with the manufacturer's protocol."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Mario Fraga","Raúl Pérez","Anna Planas"],"data_protocol":["Data Transformation - Beta values for probes with multiple technical replicates were averaged. Sex and mouse strain were inferred to confirm sample identity. Additionally, the following probes were filtered out: those masked by the SeSAMe pipeline (poor-design probes and probes with detection p-values > 0.05 in any sample), those flagged or with missing values in the “MFG_Change_Flagged” column from the Mouse Methylation BeadChip Manifest File, non-CpG probes, probes with missing values in any sample, and probes mapping to the mitochondrial chromosome."],"additional_accession":[]},"is_claimable":false,"name":"Methylation arrays (Infinium Mouse Methylation Beadchip) of microglia from young and old mice subject to microglial replacement via PLX diet","description":"Microglial replacement is emerging as a promising approach for treating age-related disorders, but effects on epigenetic age remain unclear. We examined DNA methylation changes in mouse microglia influenced by age and microglial replacement using Infinium Mouse Methylation BeadChips. We analyzed the FACS-sorted microglia of young (N=4), old (N=4) and old with microglial replacement (N=4) achieved using a PLX diet. Old microglia showed an aged epigenetic profile. Microglial depletion/repopulation, driving proliferation, led to accelerated epigenetic age. However, at the genome-wide level, repopulation reversed many aging-related changes, particularly those linked to immune and inflammatory response.","dates":{"release":"2025-12-01T00:00:00Z","modification":"2026-05-27T15:42:29.009Z","creation":"2025-09-24T14:13:09.1Z"},"accession":"E-MTAB-15631","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0002759","EFO_0005518","EFO_0003816","EFO_0003815"]}}