Analysis of Xenopus laevis foregut mesoderm+endoderm explants from RA or Rfx6 loss of function at 3 stages: NF25, NF33, NF38.

To define Retinoic Acid and Rfx6 regulated genes in Xenopus laevis foregut tissue, during developmental window of NF15 to NF38, we micro-dissected foregut explants containing both mesoderm and endoderm at stage NF15 from embryos injected with a translation blocking Rfx6 Morpholino Oligo or a control 5bp mismatch oligo, cultured explants, and harvested at NF25, NF33, or NF38 for bulk RNA-seq analysis. For RA loss of function, foregut explants containing both mesoderm and endoderm were treated with pan RAR antagonist BMS493 from NF15 to NF33, harvested either at NF25 or NF33 for bulk RNA-seq analysis. Overall design: Foregut mesoderm+endoderm explants were micro-dissected from wild-type Xenopus laevis embryos at stage NF15 and cultured to stage NF25, NF33, or NF38 (Adult Xenopus NXR_0031 obtained from National Xenopus Resource Stock Center, Woods Hole, MA; RRID:SCR_013731). Pools of n=8 foregut mesoderm+endoderm explants were harvested at 1 biological replicate. 3 such biological replicates per condition were generated. RNA was extracted using the Machery-Nagel RNA isolation kit (740955) according to manufacturer's instructions.