Work

scripts for bulk and single cell RNA seq analysis to investigate retinoic acid and FGF signaling effects in mouse gastruloids

Year: 2026

Type: article

Abstract: Axial elongation and cell fate decisions during early embryonic development are regulated by gradients of signaling molecules, such as retinoic acid (RA) and fibroblast growth factor (FGF). To assess the role of RA in vitro, studies have relied on its direct addition to the medium, which can produce teratogenic effects. Here, we examined the role of a RA precursor, retinol, on axial elongation, anteroposterior development, and FGF-dependent signaling in murine gastruloids, an in vitro model system for early embryogenesis. Rather than applying RA ectopically, we supplemented a retinoid-free medium with its precursor, retinol, prompting the cells to produce RA endogenously. Both bulk and single cell RNA sequencing data was generated at different conditions to understand how retinol can modulate cellular composition in gastruloids. Gastruloids cultured in high doses of retinol showed an enrichment of ectoderm, whereas low doses resulted in early mesoderm specification and increased FGF signaling. We further used our approach to confirm that RA signaling inhibits FGF in gastruloids. Here, the scripts used to analyze the sequencing data are provided.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.21398136