Project description:This study generated 10x Genomics Visium spatial transcriptomic profiles from mouse liver sections to investigate the effects of high-fat diet and kimchi supplementation on hepatic gene expression organization. Samples were obtained from male C57BL/6J mice assigned to normal diet (ND), high-fat diet (HFD), high-fat diet supplemented with spontaneously fermented kimchi (S-K), and high-fat diet supplemented with starter kimchi fermented with Leuconostoc mesenteroides KCKM0828 (LMS-K). The dataset was designed to assess diet-associated transcriptional changes across the liver lobule and to evaluate how kimchi intervention modulates zonation-related hepatic programs along the portal-to-central axis. Raw FASTQ files were prepared for SRA submission through GEO, and processed outputs include filtered gene-barcode matrices, HDF5 matrices, spatial coordinate files, scale factor files, tissue images, and summary reports.
Project description:We report here NGS RNA-seqencing datasets with wild-type (Chiifu) and kimchi cabbage with Arabidopsis thaliana Phytochrome B (named AtPHYB) grown under optimal temperature (22℃) condition.
Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.