Project description:Circadian rhythmicity in renal function suggests a requirement for circadian adaptations in renal metabolism. We studied circadian changes in renal metabolic pathways using integrated transcriptomic, proteomic and metabolomic analysis performed on control mice and mice deficient in the circadian clock gene Bmal1 in the renal tubule (cKOt mice). Proteins were extracted from whole kidneys of 60 mice. Of these, 30 were conditional knockouts of Arntl (Bmal1) and 30 were of control genotype. They were housed under 12-hours light/12-hours dark cycles and were sacrificed at six different time points: zeitgeber time ZT 0, ZT 4, ZT 8, ZT 12, ZT 16, ZT 20 ( ZT 0 being the time of light on and ZT 12 the time of light off). Five replicates per genotype and time point were analysed.
Project description:To search for CLOCK-controlled genes in human keratinocytes, we introduced siRNAs against CLOCK and harvested the cells at two time points, ZT 32 and 44. We speculated that those genes that were downregulated at both ZT time points may be selectively regulated by CLOCK
Project description:We mapped SMRT binding on the genome in mouse livers and found no obvious circadian rhythm. 12-weeks old C57BL/6 male mice were fed ad libum. Livers were harvested at 5 pm (ZT 10) and 5 am (ZT 22) with 4 mice in each group. Anti-SMRT ChIP was performed independently in each mouse and pooled together for deep sequencing.
Project description:Temporally restricted feeding is known to impact the circadian clock. This dataset shows the effects of temporally restricted feeding on the hepatic transcriptome. C57/B6 mice were entrained for two weeks to a temporally restricted feeding schedule. Food was made available only between ZT(CT)1 and ZT(CT)9. Mice were then released into constant darkness while food availability was still restricted and liver tissue was collected at the indicated timepoints on the second day in constant darkness. Total RNA was extracted and 5ug were submitted to the standard Affymetrix protocol for amplification, labeling and hybridization.
Project description:Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in proteomic technologies in recent years, further improvements are needed to accelerate measurement and enhance proteome coverage and quantitative performance. Previously, we demonstrated that incorporating a scanning MS2 dimension into data-independent acquisition methods (Scanning SWATH, or more generally scanning DIA) but also ion trapping, improves analytical depth and quantitative performance, especially in proteomic methods using fast chromatography. Here, we evaluate the scanning DIA approach combined with ion trapping via the Zeno trap in a method termed ZT Scan DIA, using a ZenoTOF 7600+ instrument (SCIEX). Applying this method to established proteome standards across various analytical setups, enabling intermediate to high sample throughput, we observed a 30–40% increase in identified precursors. This enhancement extended to overall protein identification and precise quantification. Furthermore, ZT Scan DIA effectively eliminated quantitative bias, as demonstrated by its ability to deconvolute proteomes in multi-species mixtures. We propose that ZT Scan DIA can be used to broaden the application in proteomics, particularly in studies requiring high quantitative precision with low sample input, post-translational modification (PTM) analysis, and high-throughput workflows.
Project description:The aim of the experiment was to identify transcripts that are regulated by LHY, a MYB transcription factor that functions as part of the Arabidopsis circadian clock. Transgenic plants carrying an ethanol-inducible copy ot the LHY gene (Alc::LHY) were irrigated with 6% ethanol at ZT 17 (17 hours after dawn). Their transcriptome was compared to that of wild-type plants exposed to the same treatment at times 0, 2, 4 and 8 hours after ethanol addition.