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:Whole genome sequencing analysis of Korean native chicken
| PRJEB44919 | ENA
Project description:Whole genome sequencing of Bangladeshi population
Project description:We performed genomic sequencing of whole-genome amplified DNA and native DNA isolated during growth in one of five conditions. We sequenced the DNA using Oxford Nanopore and compared the signals from the whole genome amplified DNA to the native DNA to infer sites at which the native DNA was methylated. The file names here are denoted via the strain name (SC419, SC452, or SC469), the growth condition (37C M9, 42C M9, 25C M9, rich media LB, 96 hours of growth), and in two cases, the replicate culture (M9_rep1 and M9_rep2)
Project description:CNV plays an important role in the chicken genomic studies,it is imperative need to investigate the extent and pattern of CNVs using array comparative genomic hybridization (aCGH) in chinese chicken breeds for future studies associating phenotype to genome architecture. we describe systematic and genome-wide analysis of CNVs loci in five Chinese indigenous chicken breeds were evaluated by aCGH. 5 Chinese native chicken were detected using ANKA broiler as reference.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:We carried out a comparative genomic analysis of 48 avian species to identify avian-specific highly conserved elements (ASHCEs). We performed genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) for three enhancer-associated histone modifications (H3K4me1, H3K27ac, H3K27me3), to investigate dynamic regulatory roles of ASHCEs in chicken development. We found that all three enhancer-associated histone marks are enriched in ASHCEs compared to the whole genome background.
Project description:To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.
Project description:Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. DNA methylation in the gene body region, especially in the internal exons, was higher than in the 5’ and 3’ flanking regions of genes.Differentially methylated region (DMR) analysis indicated widespread differences between the Leghorn and Fayoumi lines. Of particular interest, many identified DMR-associated genes were significantly enriched in immune-related groups, which indicate that DNA methylation may regulate host immune response to pathogen infection in chickens as these two genetic lines have demonstrated differential resistance to a few pathogens. This work establishes a comprehensive and precise DNA methylation pattern in chickens and lays a solid foundation for future studies on epigenetic modifications related to poultry growth, disease, and development. DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi,which were generated by deep sequencing, using Illumina GAII