Project description:Eurasian common shrews (Sorex araneus) maintain exceptionally high metabolic rates year-round, posing a significant energetic challenge during winter when food availability declines. To investigate seasonal metabolic regulation, we performed proteomic profiling of liver tissue—central to energy homeostasis—across seasons, using a bottom-up/shotgun DDA LC-MSMS proteomics analytical strategy. This approach reveals molecular adaptations that support metabolic resilience and highlights key regulatory shifts in response to environmental stress. The files and search results are labelled as: Liver_<YEAR>_<MONTH>_G_Juvanile/Adult_Mouse#1-5 Example: “Liver_2020_07_G_J2” is a liver sample collected in 2020 month 07 from juvenile mouse #2 Liver_2020_07_G_J1-5: summer 2020 Liver_2020_11_G_J1-4: fall 2020 Liver_2021_04_G_A1-5: spring 2021 Liver_2021_06_G_A1-5: summer 2021 By exploring these mechanisms, we offer novel insights into the interplay between metabolism, size, and longevity, shedding light on both the wintering strategy of the common shrew and broader mammalian physiology.
2025-10-31 | PXD068559 | Pride
Project description:WGS Listeria monocytogenes from dairy food and environmental samples.
Project description:Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min. The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. Nucleic Acids Res. 42:9383-98.
Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).
Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
