Project description:H. seropedicae wild-type or ntrC mutant were grown on three different nitrogen conditions: nitrogen limiting, ammonium shock and nitrate shock.
Project description:Monocytes were isolated from blood of Wildtype, Mir150 and TET3 knockout mice, sorted for classical and non-classical monocyte subsets. RNA seq was performed on unstimulated monocytes.
Project description:This study investigates the impact of Plin4 gene deletion on lipid metabolism in mouse liver and plasma under different dietary conditions using untargeted lipidomics. Female wild-type (Plin4+/+) and knockout (Plin4-/-) mice were fed either a control diet or a Western diet high in fat, fructose, and cholesterol. Samples included liver tissue and plasma (n = 5 per tissue type per group, total n = 40). Lipids were extracted using isopropanol, with pooled quality control samples prepared and injected regularly for signal correction. Lipidomic analysis was performed using ultra-high-performance liquid chromatography coupled to Orbitrap mass spectrometry (UHPLC-MS), with data acquired using Xcalibur and processed in Compound Discoverer and LipidSearch. Features were normalized using the SERRF algorithm, and lipid identifications were based on MS/MS fragmentation matching. This dataset provides global lipid profiles for evaluating the metabolic effects of Plin4 deletion in both normal and diet-induced obese states.
Project description:Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression. We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report on the genome-wide 5hmC patterns. Heterozygote pairs of Tet1 B6;129S4-Tet1tm1.1Jae/J mice were bought from The Jackson Laboratory (Maine USA). Heterozygotes were interbred to produce homozygous knock out males with colony mate wild type controls. Genome-wide 5hmC patterns were generated by hydroxymethyl-DNA immuoprecipitation (hmeDIP) followed by genome wide sequencing on the Ion Proton P1 sequencer.