biostudies-arrayexpressMarcela Parra VargasMus musculusR (version 3.6.0), oligo R package, arrayQualityMetrics, Bioconductor packageshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16088During 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.biostudies-arrayexpressLabeling - 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.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsGeneChip Pico Kit (Affymetrix/ThermoFisher)N/AAdipocyte Progenitor Isolation Kit (Miltenyi Biotec)GeneChip Clariom S mouse array cartridge and Affymetrix GeneTitan MultiChannel SystemReliaPrep RNA Miniprep System (Promega)GeneTitan MultiChannel Systemtranscription profiling by arrayMus musculusMarcela Parra VargasJosep Jimenez ChillaronfalseGene 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.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.2026-02-24T00:00:00Z2026-05-27T15:32:31.12Z2025-11-11T14:16:35.813ZE-MTAB-16088EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003816EFO_0003815EFO_0003969