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. Overall design: 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.)