Spatial transcriptomic profiling of livers from mice fed standard or Western diet
Spatial transcriptomic profiling of livers from mice fed standard or Western diet
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. 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. Bcl2fastq was used to convert BCL files to paired-end fastq files. No nuclei acid extraction was performed in this experiment. Visium HD WT Panel Gene Expression library preparation was performed exactly according to the manufacturer's instructions. 