Ectoderm and mesenchyme gene expression in the developing mouse face

This investigation provides a robust multi-dimensional compendium of gene expression data relevant to mouse facial development. It profiles the transcriptome of ectoderm and mesenchyme from the three facial prominences in a time series encompassing their growth and fusion. Analysis of the dataset identified more than 8000 differentially expressed genes comprising dramatically different ectoderm and mesenchyme programs. The mesenchyme programs included many genes identified in earlier analyses as well hundreds of genes not previously implicated in craniofacial development. The ectoderm programs included over a thousand genes that highlight epithelial structure, cell-cell interactions and signaling. The dataset includes 45 .cel files, DABG probability and RMA log2 expression values for each probeset, and statistics for 9457 probesets representing 8575 genes. 45 total samples, with 15 conditions sampling three ages (E10.5, E11.5, E12.5), three facial prominences (mandibular, maxillary and fronto-nasal) and two tissue layers (ectoderm or mesenchyme), with 3 biological replicates per condition. Differential expression was determined after median filter for variance with three-way ANOVA, Benjamini-Hochberg multiple testing correction本研究构建了一套稳健的多维度小鼠面部发育相关基因表达数据集汇编。本数据集绘制了小鼠三大面部突起在生长与融合全过程的时间序列转录组表达谱，涉及外胚层（ectoderm）与间充质（mesenchyme）两种组织层。对该数据集的分析共鉴定出超过8000个差异表达基因（differentially expressed genes），这些基因可分为特征差异显著的外胚层与间充质表达程序。其中间充质表达程序既包含既往研究已报道的诸多基因，也涵盖了数百个此前未被关联至颅面发育（craniofacial development）过程的新基因；外胚层表达程序则包含超过1000个与上皮结构、细胞间互作及信号传导相关的基因。本数据集包含45个.cel芯片文件，每个探针集（probeset）的DABG（Detection Above Background）概率值与RMA（Robust Multi-array Average）log2转换表达量，以及对应9457个探针集（涵盖8575个基因）的统计信息。数据集共包含45个样本，对应15种实验条件：覆盖3个胚胎发育时间点（E10.5、E11.5、E12.5）、3种面部突起（下颌突、上颌突与额鼻突）以及2种组织层，且每种实验条件均设置3个生物学重复。差异表达基因的鉴定流程为：先通过中位数过滤筛选方差，再采用三因素方差分析（ANOVA），并结合Benjamini-Hochberg多重检验校正进行统计验证。