Single Cell and Bulk RNA Sequencing Analysis on the Effects of Cytoskeletal Modulation on Stem Cell Derived Pancreatic Progenitors

We revealed that the cytoskeletal state of pancreatic progenitors can influence differentiation into multiple endodermal cell lineages. Specifically, pancreatic progenitors treated with cytoskeletal-modulating compounds show gene signatures not only of endocrine cells but also of exocrine, liver, stomach, intestine, and esophagus. We used bulk and single cell RNA sequencing to study these effects of cytoskeletal compounds on pancreatic progenitor cell fate. Overall design: Single cell RNA sequencing of pancreatic progenitor cells left untreated or treated with either Latrunculin A or Nocodazle during all of stage 4 of differentiation. Bulk RNA sequencing of stage 6 SC-beta cells at the end of differentiation that were treated with Latrunculin A during either all of stage 4 or on the first day of stage 5 only. "Biott" refers to cells that have been grown in a bioreactor as described in Velazco-Cruz et al., Stem cell reports 12.2 (2019): 351-365. "Plated_control" refers to cells that have been grown in a 6 well tissue culture plastic plate. These cells did not receive any cytoskeletal compound treatments and are therefore considered as a control. The other conditions were grown in the plated format as well.