FIGURE 1

Main experimental steps used to generate a 3D RNA profile of the catshark embryonic head (stage 17). (A) Explant dissection: the top panel shows a left side photograph of a stage 17 catshark embryo with a blue arrowhead showing the dissected explant and a dotted line delimiting its posterior boundary and the bottom panel shows a higher magnification confocal view of the explant with the posterior dissection plane. (B) Cryo-sectioning: schemes show the planes used to generate series of cryo-sections (horizontal, pink; transverse, green; sagittal, blue). The total number of sections along each plane is indicated. (C) Library construction and sequencing resulting in RNA-seq data for a total of 97 sections. (D) Visualization of expression traces along each axis for all gene models. (E) Generation of a genome-wide 3D profile with its three steps (acquisition of a confocal 3D image of the explant, generation of a digitized model and computation of digital expressions for each voxel and gene model). D, dorsal; V, ventral; Ant, anterior; Post, posterior.