{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dominik Lutter"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17271"],"description":["Intermuscular adipose tissue (IMAT) accumulation within skeletal muscle is associated with cardiometabolic disease, yet its spatial organization and molecular drivers remain poorly characterized. To map IMAT expansion within the quadriceps muscle architecture, spatial transcriptomics was performed on tissue sections from diet-induced obese male C57BL/6J mice fed a 60% kcal high fat diet (HFD) or 10% kcal low fat diet (LFD) for 20 weeks. The 10x Genomics Visium platform was used to generate spatially resolved gene expression profiles, which were integrated with immunofluorescence staining for Perilipin (adipocyte marker) and Laminin (muscle fiber boundaries) to relate transcriptional signatures to tissue morphology. This dataset enables spatially resolved investigation of gene expression changes associated with IMAT expansion in the context of diet-induced obesity."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - 10x Genomics Visium Spatial Gene Expression 3′ barcoded cDNA library-construction workflow for fresh-frozen tissue","Sequencing - Standard Illumina P5 & P 7 paired-end sequencing. BCL2Fastq pipeline version: 0.3.0 bcl2fastq version: 2.17.1.14 FastQC version: v0.10.1 101:101 base paired-end reads","Nucleic Acid Extraction - Visium Spatial Gene Expression Slide & Reagent Kit, 4 rxns, PN-1000187","Sample Collection - Seven-month-old male C57BL/6J mice were fed either a low fat diet (LFD; 10 kcal% fat; D12450J, Research Diets) or a high fat diet (HFD; 60 kcal% fat; D12492i, Research Diets) for 20 weeks. At study termination, mice were euthanized and quadriceps muscles were dissected and immediately flash-frozen in liquid nitrogen. Fresh-frozen quadriceps were cryosectioned into 10 µm cross-sections at the Helmholtz Munich Core Facility Pathology and Tissue Analytics and placed on 10x Genomics Visium spatial gene expression slides. Sections were fixed and stained with DAPI, rat anti-Laminin (1:200, ab11576, Abcam), and rabbit anti-Perilipin (1:100, #57117SF, Cell Signaling), detected with donkey anti-rabbit AlexaFluor555 (1:100, A31572, Invitrogen) and goat anti-rat AlexaFluor647 (1:100, A21247, Invitrogen). Whole-section fluorescence images were acquired on a Zeiss AxioScan 1 slide scanner at 20x magnification."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - FASTQ files and histology images were processed with Space Ranger v3.0.1 and reads aligned to the Mus musculus reference genome (GRCm39, Ensembl release 110). Downstream analysis was performed in R v4.4 using Seurat v5.3.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Not applicable","Illumina NovaSeq X"],"study_type":["spatial transcriptomics by high-throughput sequencing"],"species":["Mus musculus"],"pubmed_authors":["Dominik Lutter"],"additional_accession":[]},"is_claimable":false,"name":"Spatial transcriptomic profiling of quadriceps muscles from mice fed either standard diet or high-fat diet for 20 weeks","description":"Intermuscular adipose tissue (IMAT) accumulation within skeletal muscle is associated with cardiometabolic disease, yet its spatial organization and molecular drivers remain poorly characterized. To map IMAT expansion within the quadriceps muscle architecture, spatial transcriptomics was performed on tissue sections from diet-induced obese male C57BL/6J mice fed a 60% kcal high fat diet (HFD) or 10% kcal low fat diet (LFD) for 20 weeks. The 10x Genomics Visium platform was used to generate spatially resolved gene expression profiles, which were integrated with immunofluorescence staining for Perilipin (adipocyte marker) and Laminin (muscle fiber boundaries) to relate transcriptional signatures to tissue morphology. This dataset enables spatially resolved investigation of gene expression changes associated with IMAT expansion in the context of diet-induced obesity.","dates":{"release":"2026-07-12T00:00:00Z","modification":"2026-07-12T01:00:57.547Z","creation":"2026-07-02T14:53:01.982Z"},"accession":"E-MTAB-17271","cross_references":{"ENA":["ERP196099"],"EFO":["EFO_0002944","EFO_0004170","EFO_0030005","EFO_0005518","EFO_0003816","EFO_0004184"]}}