Extended Data Fig. 3: Gastruloids display spatio-temporal organization in the expression profiles of neural, mesodermal and endodermal marker genes.
From: Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids
a–f, The expression profiles of several genes usually expressed in the embryonic neural, mesodermal and endodermal domains were analysed by plotting RNA-seq data from the pooled gastruloids in heat maps of scaled gene expression (2 independent biological replicates per time point) (a, c, e) and/or by WISH (b, d, f). a, b, Genes usually expressed in different types of mesoderm precursors in the embryo (for example, Tcf15 in paraxial somatic mesoderm, Osr1 in intermediate mesoderm, Bra in tail bud, notochord and presomitic mesoderm, and Pecam1 in lateral plate mesoderm) were expressed in reproducible and spatially restricted domains within the gastruloids. c, d, Expression of different neural markers was detected in our RNA-seq (c). Transcripts of genes such as Lfng or Irx3 formed continuous and homogenous domains located in the central and dorsal portion of the gastruloids, reminiscent of their expression domains in the embryo (d, top panels). Genes involved in Notch signalling in neural progenitors (Hes5, Dll1) and in the terminal differentiation of neural precursors (Phox2a, Mnx1) displayed a salt-and-pepper expression pattern, consistent with the lack of an organized neural-tube structure (see also Extended Data Figs. 4a, c, 5). However, the latter mRNAs also displayed a graded distribution along the anterior-to-posterior extension of the gastruloid axis and were absent from its posterior half (empty red arrowheads). e, f, Endoderm-specific genes were also expressed in gastruloids. In particular, genes expressed in the embryonic digestive tract were consistently found on the ventral side of gastruloids. For each gene, the proportion of gastruloids displaying the reported expression pattern is shown in the upper right corner of the image, expressed as a fraction of the total number. Experimental statistics are provided in Supplementary Information dataset 3. Scale bar, 100 µm.
