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).
Project description:Studies on S. aureus sub-populations revealed that genomes are well conserved between isolates from the same lineages despite geographic, temporal and selective diversity. However, variation of hundreds of genes can occur between isolates from different lineages and these genes could be involved in interaction with host components. In this study, we aimed to investigate the diversity of secreted virulence factors in human and zoonotic S. aureus isolates from different clonal complexes. We focused on the S. aureus clonal complexes (CC) 8 and CC22 as dominant human lineages, and CC398 as dominant livestock-associated MRSA (LA-MRSA) which is disseminating rapidly. To study the diversity of secreted virulence factors, we compared their extracellular proteomes using label-free LC-MS/MS analysis. A common protein database was created based on DNA sequencing data and PAN genome IDs.
Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization
Project description:Using a pooled (n=10) zebrafish liver DNA, we generated base-resolution DNA methylation maps to document epigenetic landscape in zebrafish genome. Here we generated single-nucleotide resoultion DNA methylation map of zebrafish pooled liver sample using Reduced Representation Bisulfite Sequencing (RRBS)
Project description:We performed whole genome sequencing on four isolates of C. jejuni, two of which were closely related phylogenetically while the remaining two were phylogenetically divergent. Genomes were closed and finished. 4-plex iTRAQ experiments were performed on the four isolates after growth on solid medium for a standard time. The research questions were: 1) how closely do the protein profiles match among the four isolates, and 2) were there any results consistent with differences in regulation among isolates.
2017-08-04 | MSV000081410 | MassIVE
Project description:Amyelois transitella pooled DNA sequencing
Project description:RNA samples extracted from astrocytes cultured from wild type and Cx43 null neonatal mice were dye labeled and individually co-hybridized with a reference of labeled cDNAs pooled from a variety of tissues on eight gene arrays containing 8975 mouse DNA sequences Keywords: dose response