Effect of sample handling on gene expression in single cells of islets of Langerhans.Valentinčič, Katarina (Avtor) Jakše, Jernej (Mentor) Theis, Fabian (Komentor) batch effectsbeta cellsbioinformaticsdifferential gene expression analysisgene set enrichment analysisscRNA-seqtype 2 diabetesThis study investigates how sample preparation, storage, and processing impact gene expression analysis in single cells of pancreatic islets, with an emphasis on distinguishing technical artefacts from actual biological changes, especially in the context of Type 2 Diabetes (T2D). We found that batch effects influenced gene expression profiles using two datasets, one previously published and one new dataset. Dataset 2 showed increased stress-related gene expression, including pathways linked to the endoplasmic reticulum (ER) stress and cytokine signalling. In contrast, Dataset 1 was characterized by gene sets associated with cell proliferation, indicating possibly less stress. The study also explored the overlap between technical stress effects and T2D-related biological changes. While there were some similarities, such as increased apoptosis in specific beta cell subtypes, the overlap was limited, suggesting that technical stress does not fully replicate the complex biological changes associated with T2D. Additionally, the analysis revealed that certain technical factors, such as pre-distribution insulin content and the number of head leaks, influenced the proportions of beta cell subtypes, underscoring the importance of considering these variables in scRNA-seq studies. The findings highlight the need for careful control and interpretation of technical variability in scRNA-seq analyses to study the biological effects of T2D accurately.20242024-09-26 07:16:04Magistrsko delo/naloga162612VisID: 247067COBISS_ID: 209083651sl