Genome-wide analysis of early mouse development

Throughout the course of early development, the reliable occurrence of stereotyped events is imperative. This careful orchestration is dependent upon regulation at the level of gene expression. While all cell types derive from a single fertilized cell and share a single genome, individual cell types differentially utilize this genome. Such differential utilization is essential for the acquisition, maintenance, and modulation of cell properties. In order to better understand the molecular basis of early development, we evaluated the mRNA expression programs of both early post-implantation mouse embryos and differentiating embryonic stem cells using a cDNA microarray platform covering 74% of the mouse genome. Mining of these datasets revealed a strong association across RNA processing, modulation of the cell cycle, and chromatin organization. Genes involved in these processes demonstrated sharp regulation during well-defined biological transitions. Dominant patterns of expression with biologically separable properties were identified. The evolutionary conservation of one cluster in particular suggested a molecular basis for the alignment of the murine and fly developmental programs. Moreover, the data suggest putative gene relationships that may also have broader implications for gene networks connecting the cell cycle to the molecular repertoire of the cell. Design: Dataset is a murine embryonic developmental time course consisting of morphologically staged samples from E6.25 to E9.0 (at approximately 0.25d intervals). There two replicates of each sample and there are 13 samples in each biological replicate series. A common reference design was employed. A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions. Developmental Stage: morphologically staged samples from E6.25 to E9.0 (at approximately 0.25d intervals) Keywords: development_or_differentiation_design Using regression correlation在早期发育过程中，模式化发育事件的稳定发生不可或缺。这种精密的发育调控依赖于基因表达层面的调控。尽管所有细胞类型均源自单个受精卵细胞且共享同一套基因组，但不同细胞类型会差异化地利用该基因组。这种差异化利用对于细胞特性的获得、维持与调控至关重要。 为了更深入地解析早期发育的分子基础，本研究采用覆盖小鼠基因组74%的cDNA微阵列（cDNA microarray）平台，对植入后早期小鼠胚胎以及分化中的胚胎干细胞（embryonic stem cell）的mRNA表达谱进行了检测。对这些数据集的挖掘分析显示，RNA加工、细胞周期调控以及染色质组织之间存在显著关联。参与这些过程的基因在明确的生物学转变过程中呈现出急剧的表达调控变化。研究鉴定出了具有生物学可区分特性的主流表达模式。其中某一基因簇的进化保守性，为小鼠与果蝇发育程序的对应调控机制提供了分子依据。此外，本数据集还揭示了若干推定的基因关联，这些关联或许能为连接细胞周期与细胞分子组成的基因调控网络研究提供更广泛的启示。 实验设计：本数据集为小鼠胚胎发育时间序列样本，包含从E6.25至E9.0（间隔约0.25天）的形态学分期样品。每个样品设置2个生物学重复，每个重复系列包含13个样品。本研究采用了通用参考设计方案。发育或分化类实验设计用于检测与发育、分化或生命周期进程相关的生物学事件：其中，发育指生物体获得成熟状态的过程，分化则指细胞获得特化功能的过程。发育阶段：从E6.25至E9.0（间隔约0.25天）的形态学分期样品。 关键词：发育或分化设计（development_or_differentiation_design）、回归相关性分析