RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia

Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.同源框基因（Hox genes）是一类高度保守的胚胎空间模式形成主控调控因子，然而这类因子如何触发区域形态发生，在很大程度上仍是未解之谜。在发育中的肠道中，同源框基因可在胚胎发育早期划定小肠与大肠的身份边界，最终促成二者在形态与功能上的特化。 中肠会形成绒毛结构，而后肠则发育出扁平的脑样沟，最终分化为异质性突起。 本研究结合力学测量与数学建模，证实后部同源框基因Hoxd13可调控塑造后肠管腔的生物物理过程。进一步研究表明，Hoxd13通过转化生长因子β（TGFβ）通路，促使上皮下间充质增厚、变硬并促进其各向同性生长；上述共同作用最终导致后肠表面发生屈曲。而转化生长因子β又可促进胶原沉积，进而影响间充质的几何结构与生长模式。 据此，我们揭示了一条位于位置遗传身份下游的级联反应事件，该事件可调控后部肠道的形态发生。 为鉴定鸡胚中直接或间接受Hoxd13调控、影响后肠形态发生的基因与通路，我们对比了野生型中肠与后肠样本的中胚层转录组，以及胚胎发育第12天（E12）和第14天（E14）的过表达Hoxd13的中胚层样本。 实验中，我们先解剖组织并手动去除内胚层，随后进行RNA提取与下游处理。 通过无偏聚类分析，我们鉴定出在后肠与Hoxd13异位表达的中肠中共同差异表达的基因。 本提交内容包含批量RNA测序的原始数据（fastq.bz2格式文件）以及带有读段计数的处理后.txt文件。 实验信息已提供于用于NCBI基因表达综合数据库（NCBI GEO）提交的.xlsx元数据文件中。