Project description:CyTOF data showed that 3-HAA significantly increased the percentage of F4/80hiCX3CR1loKi67loMHCIIhi macrophage and decreased the percentage of F4/80loCD64+PD-L1lo macrophages. scRNA-seq analyses demonstrated that 3-HAA administration was proved to regulate the function of M1 macrophages, M2 macrophages, and proliferating macrophages.
Project description:<p>Salmonella Typhimurium (S. typhimurium), a gram-negative foodborne pathogen, is the leading cause of Salmonella food poisoning in humans. slyA has been demonstrated to be a critical transcriptional regulator in S. typhimurium, enabling the pathogen to survive in host cells by modulating the expression of hundreds of genes.</p><p>In this study, we used gas chromatography coupled with tandem mass spectrometry (GC-MS/MS) to investigate the potential effect of slyA on the cell metabolism of S. typhimurium. The metabolite profiling data were linked to the transcriptomic data to elucidate the possible roles of slyA in the metabolism of Salmonella. The metabolome data indicated that several glycolysis- and lipid metabolism-associated pathways, including the turnover of glycerolipid, pyruvate, butanoate and glycerophospholipid, were affected in the absence of slyA. In addition, the mRNA levels of several genes associated with glycolysis and lipid turnover were downregulated when slyA was deleted, including pagP, fadL, mgtB, iacp and yciA. Collectively, this evidence suggests that SlyA might impact glycolysis and lipid turnover in Salmonella at the transcriptional level.</p><p><br></p><p><strong>Linked Data:</strong></p><p>The transcriptomic data haa been deposited in the NCBI SRS database, access number PRJNA656165.</p>
Project description:The DNA isolated from 44 either frozen or FFPE Neuroendocrine Neoplasm (NEN) was analysed by NGS, to identify genes more likely to be subject to sequence variations among 523 cancer-related ones.
Project description:Plasma DNA from 558 malignancies, 263 benign and borderline tumors and 367 healthy control samples were collected and subjected to random short-gun whole genome sequencing.
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.