{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Marcela Parra Vargas"],"organism":["Mus musculus"],"software":["R (version 3.6.0), oligo R package, arrayQualityMetrics, Bioconductor packages"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16088"],"description":["During obesity, white adipose tissue (WAT) expands to accommodate excess energy storage. Adipocytes and non-adipocyte cells, including preadipocytes/adipocyte progenitor cells, participate in a coordinated process to remodel and expand WAT. We used microarrays to profile gene expression in preadipocytes/APCs during early-onset and HFD-induced obesity, revealing distinct depot-specific pathways associated with each condition."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Biotinylated ss-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 10 ng total RNA (GeneChip Pico Kit Manual Workflow, user guide).","Growth Protocol - Mice were housed polycarbonate cages and kept under conditions of constant room temperature (22 + 2°C), humidity (55 + 10%), and 12 h light/dark cycles (12h/12h).","Sample Treatment - Obesity models. Early-onset obesity was induced by reducing litter size during lactation—4 pups per dam (small litter, OB) versus 8 pups per dam (control, WT)—causing postnatal overnutrition. After weaning, only male pups were used, housed 5–6 per cage, and fed standard chow for 7 weeks. At 10 weeks of age, diet-induced obesity was initiated by feeding a high-fat diet (HFD, 45% fat). WT and OB mice were either maintained on chow or switched to HFD for 14 weeks, resulting in four experimental groups: WT, OB, HD, and OB-HD, all with free access to food and water.","Hybridization - Following fragmentation, 5.5ug of ds-cDNA were hybridized for 16 hr at 45C on GeneChip Clariom S mouse array cartridge. Array cartridge was washed and stained in the Affymetrix GeneTitan MultiChannel System.","Nucleic Acid Extraction - Total RNA was isolated using the ReliaPrep RNA Miniprep System (Promega).","Scaning - Array plate was scanned using the Gene Titan MultiChannel System.","Sample Collection - Preadipocytes/APCs were isolated from inguinal (iWAT) and epididymal (eWAT) fat of 6-month-old male ICR-CD1 mice as lineage-negative (CD31⁻/CD45⁻/Ter-119⁻), Sca-1⁺ cells."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Raw expression values were obtained directly from .CEL files and processed using the RMA method in the oligo R package to obtain normalized (log₂) expression values summarized at the gene level. Quality checks, including boxplots, hierarchical clustering, and principal component analyses (PCAs), were performed before and after normalization to ensure sample quality. A complete quality report was obtained using arrayQualityMetrics R package. Statistical language R (version 3.6.0) and Bioconductor packages were used for data processing and analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["GeneChip Pico Kit (Affymetrix/ThermoFisher)","N/A","Adipocyte Progenitor Isolation Kit (Miltenyi Biotec)","GeneChip Clariom S mouse array cartridge and Affymetrix GeneTitan MultiChannel System","ReliaPrep RNA Miniprep System (Promega)","GeneTitan MultiChannel System"],"study_type":["transcription profiling by array"],"species":["Mus musculus"],"pubmed_authors":["Marcela Parra Vargas","Josep Jimenez Chillaron"],"additional_accession":[]},"is_claimable":false,"name":"Gene expression data from preadipocytes (i.e., adipocyte progenitor cells, APCs) in ICR mice under conditions of early-onset and high-fat diet (HFD)-induced obesity.","description":"During obesity, white adipose tissue (WAT) expands to accommodate excess energy storage. Adipocytes and non-adipocyte cells, including preadipocytes/adipocyte progenitor cells, participate in a coordinated process to remodel and expand WAT. We used microarrays to profile gene expression in preadipocytes/APCs during early-onset and HFD-induced obesity, revealing distinct depot-specific pathways associated with each condition.","dates":{"release":"2026-02-24T00:00:00Z","modification":"2026-05-27T15:32:31.12Z","creation":"2025-11-11T14:16:35.813Z"},"accession":"E-MTAB-16088","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003815","EFO_0003969"]}}