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. 2023 Jul 21;12:e83861. doi: 10.7554/eLife.83861

Figure 7. 3D smFISH and spatial analysis of dand5 mRNA transcripts in the KV.

Figure 7.

(A) Time-course 3D analysis of dand5 mRNA transcripts by smFISH in Tg(sox17:GFP) embryos at 3, 5, 6, 7, and 8 somite stage (ss). 3D representations of dand5 mRNA (magenta), nuclei (cyan), and sox17:GFP (green) are shown. The KV surface (green) was used to mask both the dand5-Atto 565 and DAPI channels to remove nuclear staining. Spot detection was used to detect the dand5 cytoplasmic transcripts. Axes are indicated. Scale bar = 15 µm (B) The spot detection algorithm was validated in 8 ss dand5-/- embryos raised on the Tg(sox17:GFP) background. (C–E) Quantification of differences in the number of dand5 mRNA transcripts detected on the left and right sides of the KV; total number (C), at the anterior (D), and posterior (E) sides of the KV. Gray and magenta represent the left and right sides, respectively. Paired t-tests were used. The bars represent the mean values, and the dots represent individual embryos. Asterisks denote statistical significance: * corresponds to a p-value <0.05, and ** indicates a p-value <0.005.

Figure 7—source data 1. Quantification of cytoplasmatic dand5 expression by smFISH in the LRO left, right, anterior and posterior halves.