Inferring dynamic regulatory programs in non-stationary expression time courses with applications to early human neural development

We generated RNA-seq data to measure transcriptional profiles of twenty hPSC-derived NSC populations, representing distinct regions of the developing human hindbrain and rostral cervical spinal cord. These cells are differentiated using a protocol that induces collinear activation of region-specific HOX genes during exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid after varying durations of Wnt signaling, NSCs are generated with unique rostrocaudal identities that uniformly express the neuroectodermal marker Pax6 and form N-cadherin+ rosette structures in vitro. Overall design: The data consist of RNA-seq measurements taken from hPSC-derived NSCs that were exposed to CHIR99021 for differents amount of time (2-72hr) prior to retinoic acid treatment. Each time point is represented in triplicate, with the exception of 48 hours, for which one replicate (48_B1) was filtered due to excessive zero-count genes.