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. 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).