Project description:1. Comparison of Leu3 binding in vitro and in vivo 2. comparison of nucleosome occupancy between with Leu3-binding and without Leu3-binding This SuperSeries is composed of the SubSeries listed below.
Project description:The pluripotency control regions (PluCRs) are defined as genomic regions that are bound by Oct4, Sox2, and Nanog in vivo. We utilized a high-throughput binding assay to record more than 270,000 different DNA/protein binding measurements along incrementally tiled windows of DNA within these PluCRs. This high-resolution binding map is then used to systematically define the context of Oct factor binding and reveals patterns of cooperativity and competition in the pluripotency network. The most prominent pattern is a pervasive binding competition between Oct4 and the forkhead transcription factors. Like many transcription factors, Oct4 is co-expressed with a paralog, Oct1, that shares an apparently identical binding specificity. By analyzing thousands of binding measurements we discover context effects that discriminate Oct1 from Oct4 binding. Proximal Nanog binding promotes Oct4 binding, whereas nearby Sox2 binding favors Oct1. We demonstrate by cross-species comparison and by chromatin immunoprecipitation (ChIP) that the contextual sequence determinants learned in vitro are sufficient to predict Oct1 binding in vivo.
Project description:Interventions: The Drug-sensitive group:Patients were regarded as sensitive to at least one kind of the drug in vitro HDRA assay;The Drug-resistant group:Patients who were diagnosed as resistant to all agents of their chemotherapy regiments in vitro HDRA assay;The Drug-empirical group:Patients who just underwent chemotherapy empirically without the direction of HDRA
Primary outcome(s): in vitro-in vivo correlations
Study Design: Factorial
