Project description:This study investigates the gut microbiome composition and diversity in three groups of rats: control, radiation enteritis model, and treatment (TG) groups. Total DNA was extracted from stool samples, PCR-amplified targeting 16S rRNA gene variable regions, and sequenced using Illumina MiSeq or NovaSeq platforms. Downstream bioinformatics analyses included sequence quality control, denoising (DADA2/OTU clustering), taxonomic classification, alpha and beta diversity evaluation, differential species abundance analysis, and functional prediction. The processed data include ASV/OTU tables, taxonomy assignments, and sample metadata.
Project description:The rise of sample multiplexing in quantitative proteomics for the dissection of complex phenotypic comparisons has been advanced by the development of ever more sensitive and robust instrumentation. Here, we evaluated the utility of the Orbitrap Eclipse Tribrid mass spectrometer (advanced quadrupole filter, optimized FTMS scan overhead) and new instrument control software features (Precursor Fit filtering, TurboTMT and Real-time Peptide Search filtering). Multidimensional comparisons of these novel features increased total peptide identifications by 20% for SPS-MS3 methods and 14% for HRMS2 methods. Importantly Real-time Peptide Search filtering enabled a ~2X throughput improvement for quantification. Across the board, these sensitivity increases were attained without sacrificing quantitative accuracy. New hardware and software features enable more efficient characterization in pursuit of comparative whole proteome insights.
Project description:Preeclampsia is one of the most common pregnancy disorders, and characterized by insufficient trophoblast invasion and placental inflammation. RNA sequencing was performed using placental tissues collected from PE patients and control healthy pregnant women. The results showed that OTU deubiquitinase, ubiquitin aldehyde binding 2 (OTUB2) was downregulated in placenta from PE patients.
2025-08-20 | GSE303543 | GEO
Project description:ASV vs OTU mock communities
| PRJNA601852 | ENA
Project description:microbial community diversities of otu
| PRJNA820319 | ENA
Project description:Filtering microbial diversity and eDNA
Project description:Deubiquitinating enzymes (DUBs) are key regulators of cellular homeostasis, and their dysregulation is associated with several human diseases. The ovarian tumour protease (OTU) family of DUBs are biochemically well-characterised and of therapeutic interest, yet only a few tool compounds exist to study their cellular function and therapeutic potential. Here we present a chemoproteomics fragment screening platform for identifying novel DUB-specific hit matter, that combines activity-based protein profiling with high-throughput chemistry direct-to-biology optimisation to enable rapid elaboration of initial fragment hits against OTU DUBs. Applying these approaches, we identify an enantioselective fragment for OTUD7B, and validate it using chemoproteomics and biochemical DUB activity assays.