biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsJames ClelandNextSeq 2000RNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17352To test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed Visium HD spatial transcriptomics on liver tissue from male and female mice fed standard or Western diet.biostudies-arrayexpressSequencing - Libraries were sequenced on an Illumina NextSeq 2000 with one P2 100 cycles kit per slide and the following read lengths: read 1 43 cycles, read 2 75 cycles, index 1 10 cycles, index 2 10 cycles.Sample Collection - Animals were sacrificed by carbon dioxide inhalation at 38 weeks of age. To partially control for time-of-day effects, mice were sacrificed between 07:00 and 16:00 over two consecutive days, with animals from the four experimental groups processed in an alternating order. Estrous cycle stage was not assessed or controlled for in female mice. Mice were not fasted before organ collection. Half of each liver left lateral lobe was snap-frozen and stored at -80˚C. Snap-frozen liver tissue was embedded in OCT and sectioned at 10 µm thickness.Library Construction - Visium HD WT Panel Gene Expression library preparation was performed exactly according to the manufacturer’s instructions.Sample Treatment - 6 week old F1 hybrid mice derived from a Mus musculus castaneus mother and a C57BL/6J father were fed standard chow diet (Kliba # 3437) or WD (Research Diets # D16022301i; 40 kcal% non-transfat, 20 kcal% fructose and 2% cholesterol) for 32 weeks.Nucleic Acid Extraction - No nuclei acid extraction was performed in this experiment.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesJames ClelandfalseSpatial transcriptomic profiling of livers from mice fed standard or Western dietTo test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed Visium HD spatial transcriptomics on liver tissue from male and female mice fed standard or Western diet.2026-07-31T00:00:00Z2026-07-31T13:26:44.871Z2026-07-17T16:14:54.36ZE-MTAB-17352ERP201405E-MTAB-17281EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184EFO_0003969