Supplementary Materials

An interactive three-dimensional digital atlas and quantitative database of human development

Bernadette S. de Bakker, Kees H. de Jong, Jaco Hagoort, Karel de Bree, Clara T. Besselink, Froukje E. C. de Kanter, Tyas Veldhuis, Babette Bais, Reggie Schildmeijer, Jan M. Ruijter, Roelof-Jan Oostra, Vincent M. Christoffels, Antoon F. M. Moorman

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Supplementary Text
  • Figs. S1 to S4
  • Tables S1 to S3
  • Captions for data S1 to S3
  • Captions for supplementary 3D-PDFs
  • References
Data S1
Overview of all measured organ volumes per specimen. Volumes of organs and structures were determined by counting the number of pixels within the manual outline of the structure on a digital picture of a histological section, summing this number for all sections and multiplying by the voxel volume. For further details see the Morphometry section of the supplementary methods and Fig. 4. Worksheet 1: Absolute volumes. All measured volumes for the structures present in each specimen are presented here and some examples of possible graphs are given, which allows for creation of dedicated new graphs by the user to accurately describe the volume changes of each developing structure. Note that growth as presented in these graphs is interpolated from multiple specimens. Worksheet 2: Relative volumes. Here the volumes of structures are presented relative to the total embryonic volume that has been set at 1.0. This information allows interpretation of organ growth relative to the growth of the embryo. The neural tube, for example, retains a constant relative volume of approximately 10% of the total embryonic volume throughout development. Worksheet 3: Data figure 4. In this worksheet the calculated exponential growth by the developing human embryos and their neural tubes is presented, which served as basis for Fig. 4B and C.
Data S2
Organ position relative to the developing vertebrae. Our three-dimensional reconstructions permit us to unambiguously show the position of each individual thoracic and abdominal organ relative to the developing vertebrae. All organs all observations. The organ position was measured relative to the developing vertebrae (see the Topography section of the supplementary methods and Fig. 5 for further details). All organ positions measured relative to the developing vertebrae in both specimens per stage are presented here. Worksheet 2: All organs average per stage. The average organ position was calculated by averaging the vertebral level numbers of both specimens from the same Carnegie stage. These average numbers serve as basis for the graphs in worksheet 3. Worksheet 3: Graph examples. Examples of possible graphs are presented. Together with worksheet 2 this sheet allows for creation of dedicated new graphs by the user to accurately describe the changes in the relative position of each organ.
Data S3
Overview of the appearance of structures in human, mouse and chicken embryos. A comprehensive overview of the appearance of the most prominent structures in human, mouse and chicken embryos is presented. A yellow box indicates the first appearance, and sometimes disappearance, of the different organs and structures in a specimen. A green box indicates that the organ is definitely present in that specimen. Explanatory notes have been given when necessary (red triangles). The order of appearance of the distinct organs in these species agrees largely with the order reported by Butler and Juurlink (31), who based their staging exclusively on the exterior characteristics of the complete embryo. However, we found a consistent difference of approximately 1-2 stage equivalents when comparing matched mouse and human or chicken developmental stages. For further details see the Chronology and heterochrony section of the supplementary methods and Fig. S3. Worksheet 1: Human; Carnegie stage 7 - 23 (15-60 days of development). Worksheet 2: Mouse; Embryonic day 8.5 – 18. Worksheet 3: Chicken; 24 hours – embryonic day 10.

Additional Data

Files S1 (3D-PDFs)
Captions for supplementary 3D-PDFs
Stage 7 specimen 8752 (15-17 days of development)
Stage 8 specimen 8671 (17-19 days of development)
Stage 9 specimen H712 (19-21 days of development)
Stage 10 specimen 6330 (21-23 days of development)
Stage 11 specimen 6784 (23-26 days of development)
Stage 12 specimen 8505A (26-30 days of development)
Stage 13 specimen 836 (28-32 days of development)
Stage 15 specimen 3512 (35-38 days of development)
Stage 16 specimen 6517 (37-42 days of development)
Stage 17 specimen 6521 (42-44 days of development)
Stage 18 specimen 6524 (44-48 days of development)
Stage 20 specimen 462 (51-53 days of development)
Stage 21 specimen 7254 (53-54 days of development)
Stage 23 specimen 9226 (56-60 days of development)