Supplementary MaterialsS1 Fig: ICM in the absence of TE. stands for no treatment, 24h and 48h mark duration Difluprednate of treatment with MEKi inhibitor starting at E2.5. n denotes number of embryos. Figure is generated using the S2 Data.(TIF) pbio.2000737.s004.tif (210K) GUID:?F8BADE5A-6E60-459B-9650-463B09150923 S5 Fig: Testing for impact of apoptosis in any of the ICM cells. Results of simulations where in addition to our Rule 4, 20% of EPI cells undergo apoptosis at E4.5. This modification results in no significance difference with the earlier results when only misplaced PrE cells Difluprednate undergo apoptosis (compare with Fig 3). The data used to generate the figure is in S2 Data.(TIF) pbio.2000737.s005.tif (1.0M) GUID:?49BFE392-0A3D-4E2B-AF34-2E3822114325 S6 Fig: Assessing the impact of differences in FGF4 production in undetermined ICM and defined EPI cells. A. Results of the model described in the main text, where undetermined ICM and EPI are assumed to contribute equal amounts of FGF4. B. Results of simulations where undetermined ICMs contribute half as much FGF4 as EPI. In these simulations, we observed alterations in the initial specification of Epi and PrE at E3.75. Embryos with EPI, but no PrE (in addition to undetermined ICM) appear only in B, but the results at E4. 5 are the same in both cases, with ratios converging to 50%. C. and D. The means (boundaries of shaded regions) and medians (notches of the box-plots) of the fraction of cell types are shown for simulations shown in A. and B. The data used to generate this figure is in S3 Data.(TIF) pbio.2000737.s006.tif (1.2M) GUID:?C40CF966-B8FD-4F47-B43F-3178E182BC39 S1 Data: Results of the simulations, used to generate Figs ?Figs33C5. Data used to generated Figs ?Figs33C5 and S5 Fig.(XLSX) pbio.2000737.s007.xlsx (9.7K) GUID:?F4D8F67F-7AAD-49D6-82DE-223597D795D5 S2 Data: Single cell data used to generate Figs ?Figs66 and ?and77. Data used to generate Figs ?Figs66 and ?and77 and S3 and S4 Figs.(XLSX) pbio.2000737.s008.xlsx (488K) GUID:?DA175538-D01F-419C-A568-EC23933BA643 S3 Data: Data used to generate S6 Fig. (XLSX) pbio.2000737.s009.xlsx (13K) GUID:?51753B1A-CBF0-43D2-A222-FAF891DCE33A S1 Movie: Example of a successful development of p350 an blastocyst when all four rules applied (see also Figs ?Figs11 and ?and3a3a). (MOV) pbio.2000737.s010.mov (4.3M) GUID:?1C07C6CC-308F-419D-AD08-1DA497280998 S2 Movie: 3D example of the successful development of an blastocyst when all four rules are applied. The development is initialized at the 3-cell stage and goes up to 116 cells at E4.5. As in 2D, two TE cells in the simulation correspond to one real TE cell. In addition, TE cells are here shown with ? the size of ICM cells in order to be able to view the ICM. At E4.5, the PrE completely covers the EPI.(MOV) pbio.2000737.s011.mov (9.5M) GUID:?40316069-F428-4451-9F51-8F9533F86B0B S3 Movie: development of the ICM in the absence of the TE. Notice the emergence of the salt-and-pepper pattern and the effect of differential adhesion which finally results in S1 Fig.(MOV) pbio.2000737.s012.mov (1.6M) GUID:?611D3DD9-DD45-4451-9558-6509126ADB32 S4 Movie: Example of a development of an blastocyst depleted of FGF4. The ICM consists of only Nanog expressing cells (see also Fig 3bC3d).(MOV) pbio.2000737.s013.mov (4.7M) GUID:?21A659FF-FB83-478C-B80A-88E3B1056BD0 S5 Movie: Example of a development of an blastocyst in excess of FGF4. Difluprednate The ICM consists of only Gata6 expressing cells at the late blastocyst stage (E4.5). (see also Fig 3bC3d).(MOV) pbio.2000737.s014.mov (4.6M) GUID:?54E77D60-EDB6-471D-AB99-9335605A7E24 S6 Movie: Example of a development of an blastocyst in the absence of differential adhesion (Differential adhesion case). Many.