Time-course scRNA-seq of definitive endoderm directed differentiation

As part of a benchmarking study aiming to infer gene regulatory network models and transcription factor effects from time-series data, we took daily samples of pluripotent stem cells during in vitro differentiation to definitive endoderm. PSC culture and endoderm induction follow Genga et al. 2019 (Genga, R. M., Kernfeld, E. M., Parsi, K. M., Parsons, T. J., Ziller, M. J., & Maehr, R. (2019). Single-cell RNA-sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development.Cell reports,27(3), 708-718.) Fixation, tagging, and library prep follow Gehring et al. 2018 (Gehring, J., Park, J. H., Chen, S., Thomson, M., & Pachter, L. (2018). Highly multiplexed single-cell RNA-seq for defining cell population and transcriptional spaces. BioRxiv, 315333.)