Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Sequencing of actinobacteria type strains
Project description:A previously described low-fitness, high stress-resistant, variant of Listeria monocytogenes LO28 WT was subjected to an experimental evolution regime, selecting (in two parallel lines) for increased fitness in unstressed conditions. Evolved variants with increased fitness reverted to WT-like stress resistance. Whole genome sequencing and proteomics were used to identify differences between the ancestral and evolved strains.
Project description:Hypervirulent Klebsiella pneumoniae (hvKp) causes invasive infections and severe systemic inflammation. In this study, outer membrane vesicles (OMVs) derived from clinically isolated hvKp and classical K. pneumoniae (cKp) strains were characterized using an integrated proteogenomic workflow combining whole-genome sequencing and label-free LC–MS/MS proteomics. The dataset includes quantitative proteomic profiles of OMVs and whole-cell lysates together with strain-specific protein annotations for comparative analyses of OMVs cargo composition, functional annotation, and pathogenicity.
Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
2021-09-08 | PXD015184 | Pride
Project description:Genome sequencing of phylogenetically important Xanthomonas strains
| PRJNA1437458 | ENA
Project description:Whole-genome analyses of novel actinobacteria
| PRJNA524765 | ENA
Project description:Whole-genome analyses of novel actinobacteria
Project description:Whole genome Sequencing data from one L.infantum / L.tarentolae hybrid, 7 L.infantum / L.infantum hybrids, and their parental strains
Project description:We report the application of next-generation sequencing technology for transcription profile analysis of S. cerevisiae strains with different genetic background. By combining the whole genome sequence of these strains, we sought to explore the effects of genome mutations on the transcription diversities.
