Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion [RNA-Seq]

The placenta is an understudied organ that has a critical role in mammalian development. In early placental development, the essential process of trophoblast invasion establishes adequate blood flow between mother and fetus. Despite its importance, little is known about the genomic regions responsible for regulating trophoblast invasion. In order to identify enhancers that are important for regulating the process, we carried out ChIP-Seq for an enhancer-associated mark at two time points during early placental development. Combining these data with RNA-Seq data and protein interaction data allowed us to construct a gene-enhancer network describing trophoblast invasion. RNA-Seq at two time points in early placenta development (e7.5 an e9.5). There are 3 biological replicates per time point. Samples were pooled and sequenced on two lanes.胎盘是哺乳动物发育过程中发挥关键作用但研究尚不充分的器官。在胎盘发育早期，滋养层侵袭（trophoblast invasion）这一核心过程可建立母体与胎儿间的充足血液灌注。尽管该过程至关重要，但目前对于调控滋养层侵袭的基因组区域仍所知甚少。为鉴定对调控该过程具有重要意义的增强子，我们在胎盘发育早期的两个时间点，针对增强子关联标记开展了染色质免疫共沉淀测序（ChIP-Seq）实验。将该数据与RNA测序（RNA-Seq）数据及蛋白质相互作用数据相结合后，我们构建出了描述滋养层侵袭过程的基因-增强子调控网络。本研究在胎盘发育早期的两个时间点（e7.5与e9.5）开展了RNA-Seq实验，每个时间点设置3次生物学重复。将样本混合后，在两条测序泳道上完成了测序。