Effects of Oct4 depletion on BM-related gene expression during the initial stages of post-implantation amniotic sac embryoid (PASE) development.. Effects of Oct4 depletion on BM-related gene expression during the initial stages of post-implantation amniotic sac embryoid (PASE) development.

Basement membranes (BMs) are sheet-like structures of specialized extracellular matrix (ECM), which provide structural support for many tissues and play a central role in signalling. They are key regulators of cell behavior and tissue functions and defects in their assembly or composition are involved in numerous human diseases. Due to the differences between human and animal embryogenesis, ethical concerns, legal constraints, the scarcity of human tissue material and the inaccessibility of the in vivo condition, BM regulation during human embryo development remained elusive. Making use of a recently established embryoid allowed us to draw a picture of BM assembly during human embryogenesis and to examine BM disintegration during primitive streak (PS) cell dissemination. Further, we show that the transcription factor Oct4 regulates the expression of BM structural components and receptors and controls BM development during embryogenesis by regulating Akt signalling and the small GTPase Rac1. These results represent a relevant step towards a more comprehensive understanding of early human development. The deposited RNA-seq data aimed at evaluating the effects of siRNA-mediated depletion of the master transcription factor Oct4 on BM-related gene expression during initial stages of embryoid formation. Overall design: To investigate the role of the transcription factor Oct4 on BM-related gene expression during early human embryogenesis, we performed tansient, siRNA-mediated knockdown of Oct4 in WA19 human embryonic stem cells (hESC) and analysed its effect in early stage, WA19-derived post-implantation amniotic sac embryoids (PASE) at two different time points in three independent biological replicates. We then performed gene expression profiling analysis of control and Oct4-depleted samples using the data obtained from RNA-seq Comparative gene expression profiling analysis of RNA-seq data for control (WA19 hESC, siControl) and Oct4-depleted (WA19 hESC, siOct4) samples at time point 1 (0h PASE) and time point 2 (24h PASE) in three biological replicates (rep1,2,3).

基底膜（Basement Membranes, BMs）是一类特化的细胞外基质（Extracellular Matrix, ECM）片状结构，可为多种组织提供结构支撑，并在信号传导中发挥核心作用。它们是细胞行为与组织功能的关键调控因子，其组装异常或组成改变与多种人类疾病密切相关。由于人类与动物胚胎发生过程存在差异，加之伦理争议、法律限制、人体组织材料稀缺以及体内环境难以模拟，人类胚胎发育过程中基底膜的调控机制长期以来尚不明确。本研究借助新近构建的类胚胎体，阐明了人类胚胎发生过程中基底膜的组装过程，并探究了原条（Primitive Streak, PS）细胞扩散期间的基底膜降解机制。进一步研究发现，转录因子Oct4可调控基底膜结构组分与受体的表达，并通过调控Akt信号通路与小GTP酶Rac1，控制胚胎发生过程中的基底膜发育。上述研究结果为更全面地解析人类早期发育机制提供了重要进展。本数据集所提交的RNA测序（RNA-seq）数据，旨在探究小干扰RNA（small interfering RNA, siRNA）介导的核心转录因子Oct4敲降对类胚胎体形成初期基底膜相关基因表达的影响。整体实验设计：为探究转录因子Oct4在人类早期胚胎发生过程中对基底膜相关基因表达的调控作用，本研究在WA19人类胚胎干细胞（human embryonic stem cells, hESC）中开展了瞬时siRNA介导的Oct4敲降实验，并在两个不同时间点，对3次独立生物学重复的WA19来源的植入后羊膜囊类胚胎体（post-implantation amniotic sac embryoids, PASE）早期样本进行了分析。随后，我们利用RNA测序所得数据，对对照组与Oct4敲降组样本进行了基因表达谱分析；具体而言，针对3次生物学重复（rep1、2、3）中时间点1（0小时PASE）与时间点2（24小时PASE）的对照组（WA19 hESC、siControl）及Oct4敲降组（WA19 hESC、siOct4）样本，开展了RNA测序数据的比较基因表达谱分析。