Fig. 4: Neural tube profiling along the AP and DV axes.

a, Schematic of an E9.5 stage embryo, with beads corresponding to the neural tube (green) and the denoted axes along which profiling was performed (array E9.5_10). b, Heatmap showing the top 160 genes with expression patterns (row z-score-normalized, filtered for a log fold change greater than 0.05 and a false discovery rate (FDR) < 0.01; see Supplementary Table 7 for the list of genes) in the 25 generated spatial bins along the AP axis. Expression of Hox genes is highlighted (right). Scale bar, 184 µm. c, Spatial plots showing the normalized expression (bin z-score) of Hox modules (I, II, III, IV, V, VI) in the E9.5 (array E9.5_10) neural tube. Two representative genes for each module are indicated. Scale bar, 100 µm. d, Heatmap showing the top 160 genes with expression patterns (row z-score-normalized, filtered for a log fold change greater than 0.05 and FDR < 0.01; see Supplementary Table 7 for the list of genes) in the eight generated spatial bins along the DV axis. Expression of known patterned and our identified genes are highlighted. Scale bar, 40 µm. e, RNA–FISH showing validation for known (top) and our identified (bottom) patterns along the DV axis of the neural tube. A single tissue slice obtained from the posterior portion of the neural tube is shown in the images. n = 3 embryos with reproducible staining pattern for each profiled target from WT embryos. Scale bars, 50 µm. f, Schematic showing the spatial patterns of known (within the tube) and our identified (outside the tube) genes along the DV axis of the E9.5 stage neural tube.