Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46935 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
| 2140168 | ecrin-mdr-crc
Project description:The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program. Several interconnected mechanisms governing sexual commitment have been described. However, the processes that drive the subsequent differentiation and development of the gametocyte remain largely unexplored. Using chromatin immunoprecipitation followed by high-throughput sequencing we map the genome-wide occupancy of H3K36me2 and H3K36me3 during early gametocyte development and describe an association between these histone modifications and the global changes in the transcriptional program driving gametocyte development post-commitment.
2021-04-20 | GSE163432 | GEO
Project description:Understanding the molecular mechanisms controlling early cell fate decisions in mammals is a major objective towards the development of robust methods for the differentiation of human pluripotent stem cells into clinically relevant cell types. Here, we used human embryonic stem cells (hESCs) to study specification of definitive endoderm in vitro. Using a combination of whole genome expression and ChIP-seq analyses, we established a hierarchy of transcription factors regulating endoderm specification. Importantly, pluripotency factors, namely NANOG, OCT4 and SOX2 have an essential function in this network by actively directing differentiation. Indeed, these transcription factors control the expression of EOMES, which marks the onset of endoderm specification. In turn, EOMES interacts with SMAD2/3 to initiate the transcriptional network governing endoderm formation. Together, these results provide for the first time a comprehensive molecular model connecting the transition from pluripotency to endoderm specification during mammalian development. ChIP-Seq of Eomesodermin binding in human embyonic stem cells, differentiated towards an endodermal fate for 48h in chemically-defined culture media. Includes an input DNA control. Supplementary file GSE26097_README.txt contains descriptions of the raw data files and processed data files.
2011-01-25 | E-GEOD-26097 | biostudies-arrayexpress
Project description:Whole genome bisulphite sequencing of 13 human cancer samples and 9 normal controls. The main goal is to find the Diffrenetial methylated regions (DMR) at Genome wide level in different tissues and cancer types Sequencing of bisulfite converted DNA human cancer samples and normal control tissue types.
2016-01-08 | E-GEOD-52271 | biostudies-arrayexpress
Project description:The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC) is not well understood. Comprehensive molecular analyses were performed including high-pass whole-genome sequencing, targeted deep DNA sequencing, RNA sequencing, reverse-phase protein arrays, mass spectrometry-based proteomics and phosphoproteomics, and immune profiling on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking or received neoadjuvant chemotherapy (NACT) with excellent or poor response.
2020-05-27 | PXD014980 | Pride
Project description:Gastric cancer is one of the leading causes of cancer mortality worldwide, and peritoneal metastasis is a hallmark of incurable advanced gastric cancer. The identification of molecular vulnerability for such conditions is imperative to improve the prognosis of gastric cancer. Here, we comprehensively analysed cancer cells purified from malignant ascitic fluid samples and their corresponding cell lines from 98 patients, through whole-genome sequencing, whole transcriptome sequencing, methylation analyses, and genome-wide enhancer analyses.
2021-05-21 | GSE162213 | GEO
Project description:Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Methylation is a repressive modification of DNA prevalent throughout mammalian genomes yet mostly absent at CG rich stretches referred to as CGI. Here we identify their building principles by parallel genomic targeting of sequence libraries. Iterative insertions generated over 3,000 variants of genome-derived and artificial sequences at the same genomic site. Single molecule profiling of the methylation status of this collection allowed modeling the contribution of CG content and DNA binding factors towards the unmethylated state. It made the surprising prediction that the majority of CGs within endogenous islands are susceptible to methylation changes modulated by the presence of transcription factors, which is indeed confirmed by genome-wide methylation dynamics during multiple cellular differentiations. Our model further predicts blocks of constitutively unmethylated CGs independent from TF binding, which have a median size of ~300bp but are only present in half of all islands. Their constitutively unmethylated state is a hallmark of untransformed cells but their increased methylation is a specific and predictive feature of cancer. This study quantifies the two principal mechanisms governing methylation patterns in mammalian genomes. It provides a framework to interpret methylation data across normal and cancer samples and refines the concept of CpG islands. Libraries of DNA sequences were constructed either by mouse genome (129S6) or E.coli genome (NC_010473.1) subrepresentation or custom synthesis. DNA fragments were inserted into the genome of mouse embryonic stem cells by recombination mediated casette exchange (RMCE) at the B-globin locus. Methylation status of the inserted DNA sequences was profiled by bisulfite sequencing using a pair of universal primers flanking the fragments.
2014-09-30 | E-GEOD-51170 | biostudies-arrayexpress
Project description:Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis. Sequencing of bisulfite converted DNA of cancer cell line samples.
2014-09-03 | E-GEOD-56763 | biostudies-arrayexpress