SRA

This study was conducted to investigate the effects of enriching or depleting cell types in mucociliary organoids in Xenopus laevis. (1) Uninjected control embryos were compared to (2) inhibition of Notch signaling (suh-dbm) which enriches ionocytes and multiciliated cells, (3) inhibition of Notch and suppression of MCIDAS (suh-dbm + dnMCIDAS) which enriches ionocytes and depletes multiciliated cells, (4) overactivation of Notch (nicd) which suppresses ionocytes and multiciliated cells and promotes small secretory cells and basal cells, (5) knockdown of foxa1 (foxa1MO) which depletes small secretory cells. Embryos were injected at 2-4 cell stage and were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16, 25, and 32 for total RNA extraction. Overall design: The experiment was conducted in two biological replicates (embryos were derived from two different females and fertilizations). Control samples remained uninjected, embryos were injected with either suh-dbm (loss of Notch), suh-dbm and dnmcidas (loss of Notch and dominant-negative multicilin), nicd (gain of Notch by intracellular domain), or foxa1 morpholino oligonucleotides targeting the start condon of foxa1 and resulted in protein knockdown (loss-of-function). Sequencing was performed in two seperate paired-end runs to increase sequencing depth, with each run containing all samples.