Untargeted metabolomics data for pooled human plasma sample
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ABSTRACT: A pooled plasma of patients with chronic kidney disease and healthy controls analyzed by 13 individual CEs and stepped NCE 20/40/60% across 4 modes.
Project description:A pooled plasma of patients with chronic kidney disease and healthy controls analyzed by 13 individual CEs and stepped NCE 20/40/60% across 4 modes.
Project description:Hydroxyapatite (HA) has significant clinical promise for the repair of bone defects and the modification of implant material interfaces. However, after implantation, there are potential risks of chronic inflammation. Dendritic cells (DCs) are key cells in regulating chronic inflammatory responses, and their phenotype and functions are influenced by the surface structure of materials. Therefore, in order to provide some theoretical guidance for the optimal design of HA surface structures, this study tried to construct stepped structures on HA surfaces and investigate the effects of stepped structures on the cytoskeletal, cellular morphology, and mRNA expression profile of immature dendritic cells (imDCs). HA dishes with stepped structures were prepared utilizing the principle of oriented attachment growth, and subsequently used to construct in vitro cell culture models. The imDCs were observed by immunofluorescence staining to characterize their cytoskeleton structures and cellular morphology. Besides, transcriptome sequencing was used to examine the changes in the mRNA expression profile of imDCs. The results indicated that the stepped structures exposed on HA surfaces would increase the spread area of imDCs and affect the cell adhesion morphology. In addition, the results of the transcriptome sequencing revealed significant alterations in the mRNA expression profile, with differentially expressed genes (DEGs) predominantly enriched in the pathways associated with the focal adhesion signal pathway, the chemokine signal pathway, and the IL-17 signal pathway. Thus, the stepped structures could modulatethe cellular morphology and the immunological functions of imDCs by modulating the aforementioned signal pathways, including the focal adhesion pathway, the chemokine signaling pathway, and the IL-17 signaling pathway, thereby affecting the immune response process.
Project description:Lipidomics is a rapidly developing field in modern biomedical research. While LC-MS systems are able to detect most of the known lipid classes in a biological matrix, there is no single technique able to extract all of them simultaneously. In comparison with two-phase extractions, one-phase extraction systems are of particular interest, since they decrease the complexity of the experimental procedure. By using an untargeted lipidomics approach, we explored the differences/similarities between the most commonly used two-phase extraction systems (Folch, Bligh and Dyer, and MTBE) and one of the more recently introduced one-phase extraction systems for lipid analysis based on the MMC solvent mixture (MeOH/MTBE/CHCl3). The four extraction methods were evaluated and thoroughly compared against a pooled extract that qualitatively and quantitatively represents the average of the combined extractions. Our results show that the lipid profile obtained with the MMC system displayed the highest similarity to the pooled extract, indicating that it was most representative of the lipidome in the original sample. Furthermore, it showed better extraction efficiencies for moderate and highly apolar lipid species in comparison with the Folch, Bligh and Dyer, and MTBE extraction systems. Finally, the technical simplicity of the MMC procedure makes this solvent system highly suitable for automated, untargeted lipidomics analysis.
Project description:As the importance of transcriptional variation and regulation for Plasmodium becomes more apparent, advances for non-falciparum species are hindered by our reliance on natural infections to study parasite biology. Untargeted transcriptomic research is also complicated by low parasite densities and high proportions of human genetic material, highlighting the need for optimized sample processing protocols. In this study, we used a P. knowlesi culture diluted in whole blood as a mock P. vivax natural infection to compare white blood cell, rRNA-, and globin depletion methods and RNA-seq library preparation kits to create an optimized protocol for low-volume sample processing.
Project description:This study examines the transcriptional profile at the single-nuclei resolution human gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 patients with both PAD and Chronic Kidney Disease (CKD). In all libraries, muscle specimens were pooled prior to nuclei isolations were performed.