We aggregated ESCs in round-bottom microwell arrays composed of nonadhesive PEG hydrogels¹³ in epiblast induction medium comprising Activin-A, bFGF, and KSR, supplemented with low percentage (3%) Matrigel to induce epithelialization¹⁴ (Fig. 1a). The microwells allowed us to titrate the average number of cells seeded in each well, resulting in aggregates of defined size (Fig. 1b, Supplementary Fig. 1a, upper panel). The starting number of cells determined the size of the aggregate at 72 h of culture: an average of ~25 ESCs per microwell yielded aggregates with ~180 µm diameter, whereas seeding ~100 cells reached a diameter of ~230 µm (Fig. 1c). These aggregates featured a single lumen surrounded by an E-cadherin-positive polarized epithelium, displaying apical Pdx and Par6 expression (Fig. 1d–f, lower panel; Supplementary Fig. 1c). Smaller aggregates exhibited a discontinuous apical expression of aPKC surrounded by a multilayered E-cadherin-positive epithelium and multiple F-actin-labeled cavities, suggesting poor epithelialization and incomplete lumenization (Fig. 1d–f, upper panel). These results demonstrate that a critical aggregate size needs to be reached to form an apicobasally polarized epithelium with a central lumen, a phenomenon reminiscent of epiblast maturation¹⁵. When cells were aggregated in the absence of Matrigel, we detected increased cell shedding (Supplementary Fig. 1a, lower panel, white arrows) but no significant difference in aggregate diameter (Supplementary Fig. 1b). However, these aggregates composed of E-cadherin-positive cells demonstrated inverted F-actin polarity and featured multiple Pdx-positive and Par6-positive foci with no clear epithelium or lumen (Fig. 1g, Supplementary Fig. 1d). These results show that polarized epithelial aggregates of defined size can be readily generated from ESCs using hydrogel microwell arrays, and confirmed that the provision of Matrigel is critical for their lumenization and epithelialization¹⁶.Fig. 1

a Schematic representation of the workflow showing aggregation of ESCs and TSCs on PEG microwells. b Representative images showing EPI aggregates on microwells at 72 h formed from 25 cells/well (top) or 100 cells/well (bottom) showing F-actin staining by phalloidin. Scale bars: 200 µm. c Comparing minimum ferret diameters of EPI aggregates at 72 h formed from 25 or 100 cells/well. For 25 ESC and 100ESC conditions, total number of embryoids analyzed were 362 and 361, respectively. Data are collected from three biologically independent experiments. Large symbols indicate mean values of each replicate. Black lines indicate median and quartiles. d–f Confocal images of EPI aggregates formed from 25 cells/well or 100 cells/well fixed at 72 h and stained for aPKC (d), E-cadherin (e), and F-actin by phalloidin (f). Nuclei were stained with DAPI. Note multilayered epithelium in EPI aggregates formed from 25 cells/well showing discontinuous aPKC staining (white arrows) compared to single-layer epithelium in EPI aggregates formed from 100 cells/well showing continuous aPKC signal. Scale bars: 100 µm. g Confocal images of aggregates formed from 100 cells/well with or without Matrigel fixed at 72 h and stained for E-cadherin and Podocalxyin. Nuclei were stained with DAPI. Scale bars: 100 µm. h, i Confocal images of EPI aggregates formed from 100 cells/well without (h) or with (i) Matrigel, fixed at 72 h showing expression of Otx2, Oct4, Sox2, Nanog, and E-cadherin. Nuclei were stained with DAPI. Scale bars: 100 µm. j Bulk RNA-sequencing analysis of epithelialized and non-epithelialized EPI aggregates at 72 h formed from 100 cells/well, showing expression levels of pluripotency, epiblast-specific and early differentiation genes. Data are collected from four biologically independent experiments. k Representative images showing TS aggregates on microwells at 72 h formed from 25 cells/well (top) or 100 cells/well (bottom) showing ubiquitous GFP expression. Scale bars: 200 µm. l Comparing minimum ferret diameters of TS aggregates at 72 h formed from 25 or 100 cells/well. For 25 TSC and 100TSC conditions, total number of embryoids analyzed were 455 and 478, respectively. Data are collected from four biologically independent experiments. Large symbols indicate mean values of each replicate. Black lines indicate median and quartiles. m Bulk RNA-sequencing analysis of TS aggregates at 72 h formed from 100 cells/well, showing expression levels of stem cell and differentiation markers as well as key pathway agonists/antagonists. Data are collected from four biologically independent experiments. n–p Confocal images of TS aggregates formed from 100 cells/well, fixed at 72 h showing expression of E-cadherin and aPKC (n), Cdx2, Fibronectin, Laminin, and Eomes (o), Cdx2 and Ap2γ (p). Nuclei were stained with DAPI. Scale bars: 100 µm. For statistical analysis, two-tailed unpaired Student’s t-test (c, l) or multiple t-tests followed by Holm-Sidak multiple comparison test (j, m) were performed. For j, False Discovery Rate (FDR) with cutoff p value <0.5 was used to test significant differences between +matrigel and -matrigel conditions. Following P value style was used: (****) < 0.0001, (***) 0.0002, (**) 0.0021, (*) 0.0332, (ns) 0.1234. Source data are provided as a Source Data file.

Of note, affecting cytoskeletal activity by inhibiting stress fiber formation (Y-27632) and disrupting the actin network (CK-666) resulted in loss of a continuous apicobasally polarized epithelium. Interestingly, inducing stress fiber formation with LPA did not have any effect on epithelialization (Supplementary Fig. 2a, b). Moreover, blocking actin-myosin interaction (Blebbistatin), myosin activity (ML-7 and Calcyculin-A), or actin polarization dynamics (Cytochalasin-D/Latrunculin-A and Jasplakinolide) prevented formation of compact aggregates and, in some cases (ML-7 and Cyto-D), epithelialization. Interestingly, treatment with the PTEN inhibitor BpV showed a similar effect, in line with previous reports highlighting the role of PTEN in epiblast polarization¹⁷. These results suggested that actin polymerization and actin-myosin interaction play crucial roles in the polarization and epithelialization of EPI aggregates.

To test the identity of the aggregates after 72 h, we performed immunostaining for pluripotency and epiblast markers. In the absence of Matrigel, the aggregates showed a uniform expression of Otx2 and E-cadherin (Fig. 1h). Interestingly, Sox2 expression was detected in a polarized fashion in cells that showed high WNT and low TGF-β activity (Fig. 1h, Supplementary Fig. 3a), likely marking the remaining naïve pluripotent stem cells¹⁸, suggesting establishment of an naïve-to-primed axis. Epithelialized aggregates were comprised of E-cadherin+ cells organized in a columnar epithelium and were uniformly positive for Oct4 and Otx2. Expression of Sox2 and Nanog were detected at lower levels, often in a salt-and-pepper fashion. In general, Sox2+ cells in epithelialized aggregates demonstrated high WNT and low TGF-β activity (Fig. 1i, Supplementary Fig. 3b). Bulk RNA sequencing revealed low expression levels for naïve pluripotency factors Klf2/4, Dppa3, Tbx3 and higher levels of epiblast-specific genes Fgf5, Otx2, Utf1 in EPI aggregates. At this stage, transcripts that mark further differentiated states such as T, Sox1, or Sox17 were not upregulated albeit the levels were higher in non-epithelialized EPI aggregates (Fig. 1j, Supplementary Fig. 3c). Altogether, these observations suggested that ESCs could be coaxed into EPI aggregates that morphologically (i.e., lumenized/epithelialized) and transcriptionally resemble post-implantation epiblast.

In the early embryo, the epiblast develops in conjunction with extraembryonic tissues, and signaling from the extraembryonic ectoderm is involved in specifying the onset of gastrulation¹⁹. To mimic these interactions, we used the same hydrogel microwell array technology to generate TSC aggregates (Fig. 1k). On average, TSC aggregates were slightly smaller than EPI aggregates but their size at 72 h was also found to be dependent on the initial cell seeding concentration: aggregates composed of 25 cells or 100 cells reached a diameter of ~140 or ~200 µm, respectively (Fig. 1l). We detected expression of Cdx2, Elf5, and Eomes transcripts and high levels of Tfap2c (Fig. 1m), suggesting that aggregated TSCs maintain stem cell identity and get primed for differentiation²⁰. At this timepoint, genes expressed in more differentiated cell types such as spongiotrophoblast or giant cells were detected at relatively low levels (Fig. 1m), demonstrating that TSC aggregates have acquired an intermediate state, likely corresponding to extraembryonic ectoderm²¹. Importantly, TSC aggregates expressed several receptors for FGF and TGF-β pathways but not many of the ligands, in line with previous reports suggesting epiblast as source of Fgf4 and Nodal for embryonic development²². For BMP and WNT pathways, we could detect both receptor and ligand expression in TSC aggregates²³.

Unlike EPI aggregates, TSC aggregates grown in the presence of low percentage Matrigel did not lumenize (Fig. 1n). Immunostaining showed that TSC aggregates could interact with the surrounding laminin-based extracellular matrix (ECM) and deposited fibronectin at the aggregate core (Fig. 1o). Expression of the stem cell markers Cdx2, Tfap2c, and Eomes were primarily maintained on the periphery, suggesting initiation of differentiation from the core of the TSC aggregates²⁴ (Fig. 1o, p).

Next, we assembled the EPI and TSC aggregates into structures that we termed EpiTS embryoids. Individual EPI and TSC aggregates were transferred at 72–75 h to U-bottom low-attachment wells of a 96-well plate, where they fused together within a few hours (Fig. 2a, top panel). Time-lapse imaging revealed that by 120 h, T/Bra expression appeared at the aggregate interface. The size of EPI and TSC aggregates strongly influenced the timing of T/Bra expression (Fig. 2b). Embryoids composed of smaller EPI aggregates initiated T/Bra expression generally before 110 h; by 120 h, all embryoids had T/Bra-expressing cells regardless of the size of TSC aggregates they were fused to (Fig. 2a, bottom panel). On the other hand, EpiTS embryoids formed from larger EPI aggregates showed a delayed onset of T/Bra expression (Fig. 2b), with 50–70% being T/Bra-positive at 120 h (Fig. 2a, bottom panel). In addition to differences in timing, we observed a strong dependence of the initial EPI aggregate size on the T/Bra expression domain (Fig. 2c). At 120 h, embryoids formed from smaller EPI aggregates acquired a dispersed expression of T/Bra, covering almost the entire EPI compartment, whereas EpiTS embryoids formed from bigger EPI aggregates featured a restricted T/Bra expression (Supplementary Movies 1–4).Fig. 2

a Representative images showing T/Bra expression dynamics in EpiTS embryoids formed from different starting cell numbers per well (ESC/TSC). b Timelapse analysis between 78 h and 149 h with 2 h interval showing the onset of T/Bra expression. For 25/25, 25/100, 100/25, and 100/100 conditions, total number of embryoids analyzed were 26, 27, 31, and 26, respectively. Data are collected from two biologically independent experiments. Adjusted p values are: 100/25 vs. 100/100 p = 0.0013.c Coverage index of T/Bra expression calculated by division of T/Bra-positive area to EPI area. Data were collected from two biologically independent experiments. d–f Representative images at 114 h and 120 h showing T/Bra expression (d), background normalized mean intensity (e), and coverage (f) in epithelialized (+matrigel) or non-epithelialized (-matrigel) EPI aggregates, cultured in the presence or absence of TS aggregates at 120 h. For e, adjusted p values are: non-epith. vs non-epith.+TS p = 0.0384; Epith. vs Epith.+TS p = 0.0001. Data were collected from two biologically independent experiments. g, h Representative confocal images at 120 h showing T/Bra, Oct4, Nanog, Otx2, and Sox2 expression in epithelialized (g) or non-epithelialized (h) embryoids formed from 100ESC/100TSC condition. Nuclei were stained with DAPI. GFP-labeled TS cells were depicted in white. Dashed lines indicate EPI compartment. For all conditions in a–c and d–f, number of T/Bra:mCherry-positive embryoids over total number of embryoids analyzed are indicated at bottom right of a and d, respectively. Large symbols indicate mean values of each replicate. Black lines indicate median and quartiles. For all statistical analysis, one-way ANOVA followed by Tukey multiple comparison test was performed. Following P value style was used: (****) < 0.0001, (***) 0.0002, (**) 0.0021, (*) 0.0332, (ns) 0.1234. Scale bars: 200 µm. Source data are provided as a Source Data file.

To test whether the appearance of T/Bra expression was dependent on the epithelial architecture of the aggregates, or the presence of an extraembryonic compartment, we generated epithelialized (with Matrigel) and non-epithelialized (w/o Matrigel) EPI aggregates, and cultured them in the presence or absence of TSC aggregates. Almost all non-epithelialized EPI aggregates displayed T/Bra expression by 120 h, independent of the extraembryonic compartment. In contrast, epithelialized EPI aggregates alone did not initiate T/Bra expression and required co-culture with TSC aggregates (Fig. 2d, e), similar to embryo explants cultured without extraembryonic ectoderm²⁵. Moreover, the T/Bra expression domain was found to be more restricted in epithelialized embryoids (Epith.+TS) compared to non-epithelialized (Non-epith.+TS) ones (Fig. 2f).

To test whether T/Bra induction is specific to TSC aggregates and not due to any cell–cell contact, we co-cultured epithelialized EPI aggregates with aggregates composed of mouse embryonic fibroblasts (MEFs). MEF aggregates could occasionally induce T/Bra expression, albeit at much lower levels compared TSC aggregates (Supplementary Fig. 4a, b). This suggests that cellular interaction alone is not sufficient to induce T/Bra expression and that TSC aggregate-specific signaling may be necessary.

In vivo, signaling from the extraembryonic ectoderm is crucial for the initiation of gastrulation²⁶. To better understand the signaling influence of the TSC compartment in our embryoids, we replaced the cellular aggregates with cell-adhesive hydrogel microbeads (composed of denatured collagen cross-linked to dextran) coated with various (diffusible) morphogens involved in early mouse development. When coupled to EPI aggregates at 72 h, plain beads or beads coated with Fgf2, Activin-A, or Wnt3a could induce T/Bra expression, although at lower levels than TSC aggregates. Strikingly, Bmp4-coated beads reached the highest T/Bra expression level, outperforming the TSC aggregates (Supplementary Fig. 4a, b). Similarly, Bmp4 delivery increased WNT activity, even to higher levels compared to Wnt3a (Supplementary Fig. 4a, c). Notably, we did not detect any significant change in TGF-β activity for the proteins tested (Supplementary Fig. 4a, d). Transwell co-culture of epithelialized EPI aggregates with varying numbers of TSC aggregates did not induce T/Bra expression (Supplementary Fig. 4c, d), showing that physical interactions between the two cell compartment is crucial for symmetry breaking. Altogether, these results highlight a role of the epithelial architecture of EPI aggregates for T/Bra expression dynamics. EPI aggregates that are small (i.e., poorly epithelialized), or formed in the absence of Matrigel (i.e., not epithelialized), showed an extended T/Bra expression domain when coupled to TSC aggregates, suggesting uniform mesodermal differentiation, while in EPI aggregates the epithelium limits T/Bra expression to one side of the embryoids. Furthermore, TSC aggregate-specific signaling, likely via Bmp4, and physical EPI-TSC interaction are both important for the reproducible symmetry breaking and induction of T/Bra expression in epithelialized EpiTS embryoids.

Next, we performed immunostaining and confocal microscopy to characterize the tissues present in EpiTS embryoids at the onset of gastrulation. In the optimal culture condition that yielded the most restricted induction of T/Bra expression (100ESC/100TSC), we observed that the lumen collapsed by 120 h and the E-cadherin/Pdx-positive epithelium disappeared in T/Bra-positive posterior domain, while it remained in the anterior domain where the cells remained in epithelial rosettes with apical E-cadherin enrichment (Supplementary Fig. 5a, dashed box (i)). Moreover, we detected a local downregulation of laminin where some T-Bra/Snai1-double-positive cells emerged (Supplementary Fig. 5a, dashed boxes), indicating basement membrane degradation and epithelial-to-mesenchymal transition (EMT) that precede migration from the primitive streak in the embryo²⁷. Immunostaining for the pluripotency marker Oct4 revealed uniform expression in all cells of the EPI compartment, partially overlapping with T/Bra-positive cells. The expression domain of Nanog was more restricted, encircling and colocalizing with T/Bra expression³. The epiblast marker Otx2 was detected in a majority of the cells in the embryonic domain, excluding the T/Bra-positive cells. Notably, Sox2 was solely expressed opposite and excluded from the T/Bra domain (Fig. 2g). We believe that the Oct4+ T-Bra+ Nanog+ domain in these early EpiTS embryoids resembles the posterior end of the early to mid-streak embryo²⁸. Conversely, the Oct4+ Otx2+ Sox2+ domain marked the opposite end of the embryoids, suggesting maintenance of the anterior pluripotent epiblast. We did not detect Sox17-positive cells in embryoids that initiated T/Bra expression, but we could detect some Dppa3-positive cells (Supplementary Fig. 5b), likely marking primordial germ cell (PGC) progenitors²⁹.

Embryoids formed from non-epithelialized EPI aggregates showed dispersed T/Bra expression and did not demonstrate E-cadherin+ rosettes. Interestingly, Pdx expression was downregulated in the embryonic compartment. Moreover, laminin was completely absent and majority of cells demonstrated Snai1 expression, suggesting an expanded EMT-active domain (Supplementary Fig. 5c). T/Bra expression mostly colocalized with Oct4/Nanog; however, Otx2/Sox2 expression spanned a smaller domain compared to epithelialized embryoids, suggesting the loss of anterior neural progenitors at the expense of expanded posterior tissue (Fig. 2h). Moreover, we detected a higher number of Sox17-positive endoderm-like cells and Dppa3-positive PGC progenitors (Supplementary Fig. 5d), indicating an increased differentiation of posterior cell types.

Collectively, these results show that the epithelial architecture of the EPI aggregates directly influences the type of tissue that is created in embryoids. The presence of an epithelium favors limited T/Bra induction and a larger domain of anterior epiblasts that resemble E6.5 embryos. Conversely, in the absence of an epithelium in the initial EPI aggregate, the embryoids consist largely of posterior tissues and show premature differentiation towards the endoderm lineage.

The onset of gastrulation is the output of asymmetric signaling across the post-implantation epiblast and is tightly regulated by WNT, TGF-β, and BMP signaling pathways³⁰. Embryos that lack functional β-catenin³¹ or cleavable Nodal³² fail to upregulate T/Bra and are unable to undergo gastrulation. Furthermore, embryos lacking both copies of Bmp4 are arrested in development and do not express T/Bra²⁶. The dependence of the symmetry breaking dynamics on the epithelial architecture of EpiTS embryoids led us to probe the underlying signaling pathways that regulate T/Bra expression by generating EpiTS embryoids from WNT (TLC:mCherry^33,34) and TGF-β (AR8:mCherry³⁵) reporter ESC lines and by using specific pathway inhibitors.

Time-lapse analysis showed that in non-epithelized embryoids, T/Bra expression begins as early as 96 h, in contrast to epithelized ones, which show a delayed initiation at 120 h (Fig. 3a–b, upper panels; Fig. 3c). In epithelialized embryoids, we could detect an increase of WNT activity from 72 to 96 h, followed by a reduction and restriction to the embryonic-extraembryonic interface by 120 h. In contrast, non-epithelial embryoids demonstrated a progressive increase in WNT activity that was detected throughout the EPI domain (Fig. 3a–b, middle panels; Fig. 3d). On the other hand, TGF-β signaling was continuously active in both conditions, but its expression domain became restricted over time. Of note, compared to epithelialized embryoids, non-epithelialized ones showed significantly higher TGF-β pathway activity from 72 to 120 h, (Fig. 3a–b, bottom panels; Fig. 3e). These results showed that in EpiTS embryoids, both WNT and TGF-β pathways are active and their dynamics depend on the epithelial architecture of the EPI aggregate. In epithelialized embryoids, WNT and TGF-β signaling preceded T/Bra induction and are colocalized by 120 h, resembling the initial primitive streak-like domain. The signaling polarization rendered the anterior of the embryoids low in WNT and TGF-β activity (Fig. 3a, white arrows, Fig. 3b), potentially preserving the potential for anterior neural progenitors^36,37. In non-epithelialized embryoids, dispersed T/Bra expression was accompanied by elevated WNT and TGF-β activity by 120 h, resembling an expanded posterior domain observed in Dkk1^−/− and Cer1^−/−;Lefty1^−/− mutant embryos^38,39.Fig. 3

a, b Representative images showing T/Bra:mCherry (top), TLC:mCherry (middle), and AR8:mCherry (bottom) expression dynamics in epithelialized (a) and non-epithelialized (b) EpiTS embryoids between 72 and 120 h. c–e Background normalized mean intensity of T/Bra:mCherry (c), TLC:mCherry (d), and AR8:mCherry (e) in epithelialized or non-epithelialized embryoids between 72 and 120 h. Data were collected from three biologically independent experiments. For d, adjusted p-values are: Non-epith.+TS (72 h) vs Non-epith.+TS (96 h), p = 0.0168. f Representative images at 120 h showing T/Bra:mCherry expression in epithelialized embryoids treated with indicated inhibitors between 96 and 120 h. g Percentage of T/Bra:mCherry-positive epithelialized embryoids at 120 h, treated with indicated inhibitors between 72 and 96 h or 96 and 120 h. Background offset was used to set a threshold for T/Bra:mCherry expression. Adjusted p-values are: Control vs Lefty (96–120 h), p = 0.0061; Control vs Lefty (72–96 h), p = 0.0003; Control vs Noggin (72–96 h), p = 0.0033; Noggin (96–120 h) vs Dkk1 (96–120 h), p = 0.0001; Noggin (96–120 h) vs Lefty (72–96 h), p = 0.0121; Noggin (96–120 h) vs Dkk1 (96–120 h), p = 0.0001; Noggin (96–120 h) vs Dkk1 (72–96 h), p = 0.0006; Dkk1 (96–120 h) vs Lefty (96–120 h), p = 0.0325. h Timelapse analysis between 78 and 192 h with 2 h interval showing the onset of T/Bra expression. For control, Dkk1, Lefty, Noggin conditions, total number of embryoids analyzed were 23, 18, 15, 20, respectively. Data are collected from a single experiment. Adjusted p-values are: Control vs Dkk1, p = 0.0002; Noggin vs Dkk1, p = 0.0007. i, j Quantification of coverage index of T/Bra:mCherry expression (i) and EPI compartment area (j) at 120 h in epithelialized embryoids treated with indicated inhibitors. For i, adjusted p-values are: Control vs Dkk1 (72–96 h), p = 0.0123; Control vs Lefty (72–96 h), p = 0.0010; Control vs Lefty (96–120 h), p = 0.0009; Control vs Noggin (96–120 h), p = 0.0300. For j, adjusted p-values are: Control vs Lefty (72–96 h), p = 0.0276; Dkk1 (72–96 h) vs Lefty (96–120 h), p = 0.0049; Noggin (72–96 h) vs Lefty (96–120 h), p = 0.0021. k Representative images showing T/Bra:mCherry expression in epithelialized embryoids treated with indicated small molecule inhibitors between 96 and 120 h. l Percentage of T/Bra:mCherry-positive epithelialized embryoids at 120 h, treated with indicated inhibitors between 96 and 120 h. All embryoids were formed from 100ESC/100TSC condition. For all conditions in a–e, f, g, i, j, and k, l number of mCherry-positive embryoids over total number of embryoids analyzed are indicated at bottom right of a–b, f, and k, respectively. Large symbols indicate mean values of each replicate. Black lines indicate median and quartiles. For all statistical analysis, one-way ANOVA followed by Tukey multiple comparison test was performed. For g, i, and j significance was calculated in comparison to control. Following P value style was used: (****) < 0.0001, (***) 0.0002, (**) 0.0021, (*) 0.0332, (ns) 0.1234. Scale bars: 200 µm. Source data are provided as a Source Data file.

To test whether gastrulation-like processes observed in epithelialized EpiTS embryoids involve mechanisms similar to those observed in the embryo, we inhibited the above pathways by adding Dkk1 (i.e., a WNT inhibitor), Lefty (TGF-β inhibitor), and Noggin (BMP inhibitor) between 72 and 96 h or 96 and 120 h, respectively. Inhibition of WNT and TGF-β pathways in both time windows greatly reduced the number of embryoids that upregulate T/Bra. However, BMP inhibition by Noggin only between 72 and 96 h significantly lowered the percentage of T/Bra+ embryoids by 120 h (Fig. 3f, g). Dkk1-treated EpiTS embryoids exhibited a delayed T/Bra expression compared to nontreated or Noggin-treated ones (median ~140 versus ~125 h) (Fig. 3h). Furthermore, we observed more restricted T/Bra expression in the presence of the inhibitors, which was more pronounced in the cases of Dkk1 and Lefty (Fig. 3i). Interestingly, early treatment with these inhibitors significantly reduced the total embryoid size, an effect that was more prominent when BMP signaling was inhibited (Fig. 3j). Treatment with the small molecule inhibitors XAV939 (i.e., a WNT inhibitor), SB431542 (TGF-β inhibitor), and LDN193189 (BMP inhibitor) resulted in a more pronounced reduction of T/Bra expression; SB431542 and XAV939 treatment led to a complete loss of T/Bra expression, while a small percentage of LDN193189-treated EpiTS embryoids still expressed T/Bra, yet with a domain that was spatially restricted (Fig. 3k, l). Altogether, these results demonstrate a crucial role of WNT and TGF-β signaling in the induction and level of T/Bra expression in EpiTS embryoids between 72 and 120 h. In contrast, the BMP pathway was shown to have an effect on the overall growth of embryoids, with a smaller effect on T/Bra expression between 96 and 120 h.

Previous embryoid models involving ESCs and TSCs in ETS embryos¹¹ did not recapitulate the axial patterning of the early embryo. In our hands, ETS embryos could be generated at frequency (corresponding to multicellular aggregates comprising an embryonic and extraembryonic compartment) of 6.07% (n = 34/560) (Supplementary Fig. 6a). The ETS embryos expressed epiblast markers Oct4 and Otx2 at 120 h (Supplementary Fig. 6b). To test whether post-gastrulation developmental stages could be achieved in ETS embryos, we adopted our EpiTS embryoid culture approach by placing individual ETS embryos in U-bottom 96-wells. T/Bra expression was found to be highly variable, with some tissues showing a dispersed and others a more localized expression by 120 h (Supplementary Fig. 6c). When cultured until 240 h, ETS embryos with small embryonic-to-extraembryonic ratio were overgrown by TSC aggregates, and ETS embryos that were small in size (<200 µm) did not grow further. Interestingly, we observed that ETS embryos that upregulated T/Bra and had a larger embryonic compartment occasionally underwent axial elongation, suggesting that when grown in ECM- and serum-free culture conditions, these embryoids might reach post-gastrulation stages (Supplementary Fig. 6d).

When 120 h old EpiTS embryoids were cultured in N2B27 medium with no additional growth factors, the embryonic compartment began to elongate (Fig. 4a, b). While epithelialized EPI aggregates alone remained spherical, non-epithelialized ones elongated efficiently⁴⁰ (Supplementary Fig. 7a). The EPI compartment in EpiTS embryoids grew significantly over time, while the size of the TSC aggregates did not change markedly (Fig. 4c), suggesting that growth of extraembryonic compartment is not required for the elongation of the EPI domain. To quantify the dynamics of elongation, we performed image analysis to determine the axial length and elongation index of the embryoids (Supplementary Fig. 7b). This analysis revealed that in both epithelialized and non-epithelialized embryoids, the axial length and the elongation index significantly increased from 120 to 168 h (Fig. 4d, Supplementary Fig. 7c). EpiTS embryoids formed from non-epithelialized (or smaller) EPI aggregates were significantly more elongated at 144 h (Fig. 4d, Supplementary Fig. 7d, e), suggesting a role for the size and epithelial architecture of the starting EPI aggregate on the elongation dynamics (Supplementary Movies 5,6).Fig. 4

a, b Representative images showing T/Bra:mCherry (top), TLC:mCherry (middle), and AR8:mCherry (bottom) expression dynamics in epithelialized (a) and non-epithelialized (b) EpiTS embryoid between 120 and 168 h. c–e Quantification of total EPI vs TS area (c), elongation index (d), and background normalized T/Bra:mCherry mean intensity (e) in epithelialized or non-epithelialized embryoids between 120 and 168 h. For elongation index quantification, TS subtraction was performed. Data was collected from three biologically independent experiments. For d, adjusted p-values are: Epith.+TS (144 h) vs Epith.+TS (168 h), p = 0.0002. For e, Epith.+TS (144 h) vs Non-epith.+TS (144 h), p = 0.0277. f Representative confocal images showing Sox1, Pax6, T/Bra, Foxa2 (top panel) Six1, Eya1 (bottom panel) immunostainings at 168 h in epithelialized embryoids. g, h Representative confocal images showing Sox1, Tuj1, Sox17 (top panel), and mCherry, Otx2, Tuj1 (bottom panel) immunostainings at 168 h in epithelialized (g) or non-epithelialized (h) embryoids. Nuclei were stained with DAPI. TS cells were depicted with dashed line. All embryoids were formed from 100ESC/100TSC condition. For all conditions in a–e, number of mCherry-positive embryoids over total number of embryoids analyzed are indicated at bottom right of a, b. Large symbols indicate mean values of each replicate. Black lines indicate median and quartiles. For all statistical analysis, one-way ANOVA followed by Tukey multiple comparison test was performed. Following P value style was used: (****) < 0.0001, (***) 0.0002, (**) 0.0021, (*) 0.0332, (ns) 0.1234. Scale bars: 200 µm. Source data are provided as a Source Data file.

In embryoids generated from epithelialized tissues, T/Bra expression peaked around 144 h and gradually declined until 168 h, when it became restricted to the elongating tip and then trailed behind in a short stripe of cells. In contrast, non-epithelialized embryoids showed a constant decrease in the intensity and size of the T/Bra domain with increasing elongation (Fig. 4e, Supplementary Fig. 7f). WNT signaling was active in almost all embryoids and marked the T/Bra-expressing tip with no significant change in activity levels until 168 h (Supplementary Fig. 7g, h). In epithelialized embryoids, WNT activity reappeared at the anterior domain (Fig. 4a, b, middle panels, white arrows), resembling the TCF/LEF reporter activity in the tail and midbrain/hindbrain of E8.5 embryos⁴¹. Overall, TGF-β pathway activity was found to be lower and in close proximity to the extraembryonic compartment, excluded from the elongating tip (Fig. 4a, b, bottom panels; Supplementary Fig. 7i, j).

To better understand the underlying mechanism of axial morphogenesis in our embryoids, we investigated the roles of the WNT, TGF-β, and BMP pathways by inhibiting their activity between 96 and 120 h. In general, treatment with inhibitors resulted in significant size reduction by 168 h (Supplementary Fig. 8a). Dkk1 and Lefty led to a reduction of T/Bra-positive embryoids, compared to Noggin. Embryoids treated with Lefty exhibited small clumps of T/Bra-positive cells, while Dkk-treated ones showed a more scattered expression throughout the body of the structure (Supplementary Fig. 8b). In Noggin-treated embryoids, T/Bra expression was retained within a larger domain compared to untreated or Dkk1/Lefty-treated ones (Supplementary Fig. 8c). Notably, the elongation frequency was found to be significantly higher in the presence of Noggin (Supplementary Fig. 8d, Supplementary Movies 7–10). It is conceivable that excessive BMP signaling from the extraembryonic ectoderm could impair axial elongation, and treatment with Noggin could mitigate this effect, consistent with the antagonistic role of BMP4 on axial elongation of gastruloids⁴². In these embryoids, T/Bra-positive cells were often organized into longer stripes that co-expressed FoxA2, suggestive of a more developed notochord or an anterior mesendoderm (AME)-like structure (Supplementary Fig. 8e). In support of this, we detected higher expression levels of T/Bra, Shh, FoxA2, and Gsc with Noggin-treated compared to untreated embryoids (Supplementary Fig. 8f), in line with previous reports defining a role for Noggin in proper notochord formation⁴³.

At 168 h, epithelialized embryoids acquired an expanded neural identity, as evidenced by Sox1 expression spanning from the elongated tip towards the opposite end. Interestingly, we could detect polarized expression of Pax6 and T-Bra/Foxa2, all partially overlapping with Sox1 expression, suggesting a dorsal–ventral organization similar to the developing neural tube⁴⁴. Furthermore, the neural tissue was flanked by Six1+ Eya1+ paraxial mesoderm derivatives (Fig. 4f), suggesting an organization across a medio-lateral axis. We detected numerous Tuj1-positive neurons within Sox1-positive rosettes located on the opposite end of the elongated tip. The rosettes and neurons showed high WNT activity colocalized with Otx2 expression, indicating establishment of an anterior–posterior axis to include a ‘brain-like’ tissue. Moreover, only few Sox17-positive cells were found scattered in the vicinity of the extraembryonic domain, suggesting poor endoderm differentiation (Fig. 4g). In contrast, non-epithelialized embryoids showed a smaller domain of Sox1 expression comprising comparable numbers of Tuj1-positive neurons with relatively short axonal projections. Compared to epithelialized embryoids, the Otx2 expression domain was more restricted and showed low levels of WNT activity. Tuj1-positive neurons were also located away from the WNT-positive elongated tip. Interestingly, the expression domain of Sox17 in these embryoids was much larger and located at the anterior end of the embryoids colocalizing with Foxa2 (Fig. 4h, Supplementary Fig. 8g), similar to endoderm tissue seen in gastruloids⁶. Collectively, these data demonstrate the capacity of EpiTS embryoids to spontaneously undergo axial morphogenesis to establish multi-axial patterning. Importantly, the presence or absence of an epithelium in the starting EPI aggregate directly influences the elongation dynamics as well as the proportions of the tissue types that are generated.

To shed light on the cell-type composition and diversity of EpiTS embryoids, we performed single-cell RNA-sequencing (scRNA-seq) analysis between 120 and 192 h (Fig. 5). We could identify that from 120 h onwards, cells mapping to an epiblast-state gradually differentiated into ectoderm or mesendoderm lineages (Fig. 5a, germ layers). Primordial germ cells and extraembryonic tissue had a distinct transcriptional identity that segregated away from the germ layers observed in our embryoids. RNA velocity on extraembryonic cells showed no clear temporal differentiation trajectory; however, we identified distinct cell populations that suggested a compartmentalization within the extraembryonic tissue (Fig. 5a, extraembryonic). At 120 h, the majority of the extraembryonic tissue had chorion identity (Cdx2, Elf5, Eomes, Esrrb) and expressed Bmp4, supporting involvement of BMP signaling for the initiation of gastrulation-like events in our embryoids. Interestingly, we detected Furin and Pcsk6 expression that could suggest the processing of embryonic Nodal by the extraembryonic tissue⁴⁵. We further identified clusters of cells that map to ectoplacental cone (Fgfbp1, Ascl2) or labyrinth progenitors (Gjb2, Dlx3, Ovol2) that demonstrate multipotentiality of chorionic ectoderm. At later stages of culture, we detected trophoblast giant cells (Hand1, Ctsq, Prl2c2) and a few spongiotrophoblast cells (Tpbpa, Flt1) (Fig. 5b, extraembryonic markers, Supplementary Fig. 9a–d), in line with previous in vitro TSC differentiation data⁴⁶.Fig. 5

a UMAP plots showing cell types, RNA velocity overlayed stages, and datasets of origins in germ layers, mesendoderm, epiblast + ectoderm, and extraembryonic clusters. b Heatmap plot of selected marker genes from mesendoderm, epiblast + ectoderm, and extraembryonic clusters. PGC primordial germ cells, Lat. lateral, Mes. mesoderm.

A closeup on the mesendoderm cluster revealed complex differentiation trajectories (Fig. 5a, mesendoderm). At 120 h, the majority of cells had a primitive streak identity (T, Mixl1, Wnt3), that progressively branched to give rise to endoderm (Sox17, Spink1) and notochord (Noto, T, Shh) tissues via an anterior primitive streak-like population (Foxa2, Gsc). Cells mapping to the nascent mesoderm (Mesp1, Hoxb1) diverged into two distinct trajectories: the anterior portion gave rise to cardiac mesoderm (Myl7, Gata4, Hand2) and cardiomyocytes (Ttn, Nkx2-5, Mef2c)⁷, while the posterior nascent mesoderm cells differentiated towards paraxial mesoderm (Msgn1, Tbx6, Meox1). The paraxial mesoderm further diverged into somitic (Meox2, Pax3, Uncx), posterior lateral mesoderm (Msx2, Foxf1, Hoxc6) or intermediate mesoderm (Osr1, Gata3, Wt1) tissues. From 168 to 192 h of culture, the abovementioned mesoderm populations gave rise to more differentiated pharyngeal mesoderm (Prrx1, Isl1, Tbx1), sclerotome (Pax1), and dermomyotome (Dmrt2) cells (Fig. 5b, mesendoderm markers, Supplementary Fig. 10a, b).

A detailed RNA-velocity analysis of the ectoderm cluster revealed that between 120 and 144 h, epiblast cells (Oct4, Nodal) gave rise to spinal cord tissue (Sox1, Pax6, Hoxb7/8/9) (Fig. 5a, epiblast + ectoderm). We noted a striking compartmentalization among the cells of the spinal cord, with differentiation towards dorsal (Wnt1, Dbx2, Pax7) and ventral (Olig2, Foxa2, Shh) cells of the neural tube. On a second trajectory, epiblast cells differentiated to generate midbrain/hindbrain tissue. The lower expression level of midbrain markers (En1/2, Pax5) and higher expression level of hindbrain markers (Egr2, Irx2, Epha7, Fst) could suggest that the ‘brain-like’ tissue generated in the embryoids was primarily of hindbrain origin. In support of this, we detected Hoxa2, Hoxb1/2, and Cyp26 expression in the hindbrain-like tissue, while more posterior Hoxa3/b3 and Hoxb4 were excluded from this region (Fig. 5b, epiblast + ectoderm markers; Supplementary Fig. 11a, b), suggesting that the hindbrain tissue in our embryoids corresponds to rhombomeres 1–6⁴⁷. At later stages, we detected neural stem cells (Pou3f3, Ascl1, Nes) that either had midbrain/hindbrain (Zic1/5, Msx3) or spinal cord (Hoxa4/b4) identities. These neural stem cells generated dorsal interneurons (Lhx1/5, Pou4f1) and ventral motor neurons (Isl1/2, Nkx6-1 Phox2a/b) at both spinal cord (Hoxb7/8/9) and hindbrain (Lhx2/9, Barhl1/2) levels (Supplementary Fig. 12a–d), revealing a remarkable recapitulation of the cell-type diversity similar to the in vivo situation⁴⁸.

We then used the scRNA-seq dataset to systematically assess the effect of the initial epithelial architecture of embryoids on the resulting cell-type diversity. A comparative analysis of epithelialized and non-epithelialized embryoids showed that several tissue types, including cardiac mesoderm, definitive endoderm, and pharyngeal mesoderm derivatives, were almost exclusively found in non-epithelialized embryoids (Fig. 5e, Supplementary Fig. 13a, b). Moreover, the neural tissues in non-epithelialized embryoids were shown to be composed of spinal cord tissue. Conversely, midbrain/hindbrain tissue, brain-specific neural stem cells, and their respective neurons were only detected in epithelialized embryoids (Supplementary Fig. 12e). These results demonstrate that the epithelial architecture of initial EPI aggregates has a direct impact on embryonic developmental trajectories and promotes neural differentiation in embryoids.

Mouse embryonic stem cells (SBr line⁵⁸) were cultured at 37 °C in 5% CO₂ in medium composed of DMEM + Glutamax (#61965-026), 10% ES cell-qualified FBS (#16141-079), 1 mM sodium pyruvate (#11360-070), 1× MEM nonessential aminoacids (#11140-035), 0.1 mM 2-mercaptoethanol (#31350-010), and 1000 u/ml Pen/Strep (#15140-122) supplemented with 3 µm GSK3i (#361559), 1 µm MEKi (#S1036), and 0.1 µg/ml LIF (in house preparation). Cells were routinely passaged every 2–3 days by seeding 8000–9000 cells/cm² and every 20 passages a fresh vial was thawed. Cells were tested and confirmed free of mycoplasma. Mouse trophoblast stem cells (TS:GFP line⁵⁹) were cultured at 37 °C in 5% CO₂ in TS medium composed of RPMI 1640 + Glutamax (#61870-010), 20% ES cell-qualified FBS (#16141-079), 1 mM sodium pyruvate (#11360-070), 0.1 mM 2-mercaptoethanol (#31350-010), and 1000 u/ml Pen/Strep (#15140-122). TS medium was conditioned on irradiated MEFs for 3 days and stored at −20 °C. This was repeated three times for one batch of irradiated MEFs. Aliquots of TS conditioned medium (TSCM) were thawed and mixed 3:1 with fresh TS medium before cell passaging. 50 ng/ml Fgf4 (#100-31) and 1 µg/ml Heparin (#H3149) were added to make final TS medium. TS cells were routinely passaged every 2–3 days by seeding 5000–6000 cells/cm² and every 20 passages a fresh vial was thawed. MEFs were prepared in house and stocks were prepared at passage 1. They were cultured in TS medium with no additional growth factors. For the co-culture experiments, MEFs from passages 4–7 were used. Cells were tested and confirmed free of mycoplasma.

N2B27 medium was prepared by 1:1 mixing of DMEM/F12+Glutamax (#31331-028) and Neurobasal (#21103-049) with the addition of 0.5× N2 supplement (#17502001), 0.5× B27 supplement (#17504001), 0.5× Glutamax (#35050-038), 1 mM sodium pyruvate (#11360-070), 1× MEM nonessential aminocacids (#11140-035), 0.1 mM 2-mercaptoethanol (#31350-010), and 1000 u/ml Pen/Strep (#15140-122). 12 ng/ml Fgf2 (#PMG0035), 20 ng/ml Activin-A (#338-AC), and 1% KSR (#10828-010) were added to make final EPI differentiation medium (EPIdiff). TS differentiation medium (TSdiff) was prepared by 1:1 mixing of N2B27 and TS medium supplemented with 25 ng/ml Fgf4 (#100-31) and 500 ng/ml Heparin (#H3149).

Poly(ethylene glycol) (PEG) microwells with 400 µm well diameter (121 wells per array) were prepared on 24-well plates as previously descrbed¹³. Microwells were equilibrated with 50 µl of either EPIdiff (for ES cells) or TSdiff (for TS cells) for at least 30 min at 37 °C. Mouse ES and TS cells and were dissociated to single cells with Accutase (#A11105-01) or TrypLE (#12605-028), respectively. Cells were then centrifuged at 112 × g for 5 min and washed twice with 10 ml PBS at 4 °C. Cells were resuspended in cold EPIdiff (for ES cells) or TSdiff (for TS cells) and suspension of 484.000 cells/ml was prepared. 35 µl of the suspension was added dropwise on microwell arrays to have 100–150 cells/well. Seeding was done at 37 °C for 15 min. Growth factor reduced Matrigel (#356231) was diluted in cold EPIdiff or TSdiff to 3% or 2% (v/v), respectively. The medium was vortexed and 1 ml was slowly added from the side of the well, avoiding direct addition from the top of the microwell arrays. Plates were kept at 37 °C in 5% CO₂ for at least 72 h before further processing.

At 72–75 h of culture, aggregates on microwell arrays were flushed out and transferred to non-tissue culture treated 10 cm plates in 10 ml warm N2B27 medium. Single EPI and TSC aggregates were picked in 10 µl and transferred to low adherent U-bottom 96-well plates (#COR-7007). 170 µl of N2B27 medium was added on top. At 96 and 120 h, 150 µl of medium was replaced with fresh N2B27 and EpiTS embryoids were generally kept until 168 h. Protein inhibitors Lefty (#746-LF-025), Noggin (in house preparation), Dkk1 (#5897-DK-010) were added at indicated timepoints at 200 ng/ml final concentration. Small molecule inhibitors; SB431542 (#S4317), XAV939 (#S1180), LDN193189 (#SML0559) were added at indicated timepoints at 10 µm, 10 µm, and 1 µm final concentrations, respectively.

ETS embryos were generated as previously described¹¹. Briefly, mESCs were dissociated into single cells by accutase and washed with PBS. In parallel, TSCs were dissociated with trypsin into small clumps of 4–5 cells and washed with PBS. Five thousands mESCs and 5000 TSC clumps were counted and mixed in total of 120 µl Matrigel. From the suspension, 15 µl drops were casted onto µ-Slide 8-well plates. After gelation, 400 µl of TSdiff medium was added and plates were kept at 37 °C in 5% CO₂ for 24 h. Next day and on third day medium was changed with 400 µl fresh TSdiff.

EPI aggregates were formed in the presence of Matrigel with following inhibitors until 72 h: 1 µm LPA(#L7260), 10 µm Y27632 (#72302), 10 µm Blebbistatin (#72402), 1 µm ML-7 (#4310), 5 mm Calyculin-A (#9902 S), 100 nm Cytochalasin-D (#250255), 1 µm Latrunculin-A (#L5163), 100 nm Jasplakinolide (#J4580), 50 µm CK-666 (#SML0006), 25 µm BpV (#S8651).

For bead experiments, Cytodex 3 microcarriers (#17048501) were resuspended in HBSS (Ca⁺⁺, Mg⁺⁺) at 40,000 beads/ml concentration. Six hundred beads were transferred in 0.5 ml eppendorfs and Fgf2 (#PMG0035), Activin-A (#338-AC), Wnt3a (in house preparation), or Bmp4 (#120-05ET-100) was added at 25 µg/ml final concentration. Beads were incubated at 4 °C overnight. Next day, beads were washed repeatedly to reach 1:250,000 dilution in N2B27 and transferred in 10 µl to low adherent U-bottom 96-well plates together with epithelialized EPI aggregates.

For transwell experiments, EPI aggregates were placed in 190 µl to low adherent U-bottom 96-well plates and 1, 3, or 5 TSC aggregates were placed in transwells on top (#CLS3374). Forty microliters of medium was added to cover TSC aggregates. At 96 h, 180 µl of medium was replaced with fresh N2B27.

EpiTS embryoids were washed with PBS and fixed with 4% PFA for 2 h at 4 °C. PFA was removed by three serial washes of 20 min at room temperature. Blocking was performed in blocking solution (PBS + 10%FBS + 0.3% Triton-X) for 1 h at room temperature. Primary antibodies (see Supplementary Table 1) were incubated for at least 24 h at 4 °C in blocking solution. Next day, primary antibodies were removed by three serial washes of 20 min at room temperature. Secondary antibodies were incubated for 24 h and next day embryoids were washed and mounted on glass slides in mounting medium. Confocal images were taken using an LSM700 inverted (ZEN software, Zeiss) with EC Plan-Neofluar ×10/0.30 or Plan-Apochromat ×20/0.80 air objectives.

All images were processed using algorithms developed in Image J (version 2.0.0-rc-69/1.52n). Brightfield, GFP (for TS cells), and mCherry (for T/Bra) channels were used as input. Thresholding and segmentation was performed sequentially for each channel. An embryoid was considered positive if the signal for the reporter was at least 30% more than the background and had an area of at least 1500 µm². Area of EPI domain was calculated by subtraction of the area of the object identified in GFP channel from the area of the object identified in brightfield channel. For the calculation of the anterior EPI domain, area of the object identified in mCherry channel was subtracted from the EPI area. T/Bra coverage index was calculated by dividing area of the object identified in mCherry channel to the EPI area. For morphology measurements, brightfield images were thresholded and segmented. Maximum inscribed circle function was used to fit circles in the identified object. Axial length was determined by connecting centers of the fit circles. Elongation index was calculated by dividing axial length to the diameter of the maximum inscribed circle. All image analysis codes are available upon request. Data was analyzed by using Microsoft Excel and GraphPad Prism.

RNA was extracted with the RNeasy Micro kit (QIAGEN), according to manufacturer’s instructions and quantified with a spectrophotometer. One microgram of RNA was reverse transcribed with the iScript cDNA Supermix (#1708890). cDNA was diluted 1:5 and amplified by using Power SYBR Green PCR Master Mix. qPCR was run with a 7900HT Fast PCR machine (#4329001), using Power SYBR Green PCR Master Mix (Applied Biosystems), with an annealing temperature of 60 °C. Gene expression was normalized on Gapdh expression. Relative fold expression was calculated with the 2−ΔΔCT method. Primers used are indicated in the Supplementary Table 2.

EPI and TSC aggregates (formed from 100 cells/well condition) were lysed with 200 µl trizol, followed by addition of 70 µl of chloroform to trigger phase separation and then the aqueous phase was collected. The extraction process was repeated a second time, and an equal volume of isopropanol was added to precipitate the RNA, which was collected by centrifugation at 20,000 × g for 30 min. The pellet was washed with 15 mM sodium acetate in aqueous 70% ethanol, followed by salt-free 70% ethanol, before picking up in RNAse free water. RNA quantity and quality were assessed on nanodrop, qubit, and Agilent TapeStation 4200 profiling, and showed absorbance ratios 260/280 of 1.85 ± 0.12 and RNA integrity numbers (RIN) of 9.9 ± 0.2 (average ± SD), supporting good purity and absence of degradation. TruSeq stranded mRNA LT libraries were prepared according to Illumina protocol 15031047 Rev. E, starting from 300 ng of RNA, quantified by qubit DNA HS, profiled on TapeStation 4200, and sequenced on an Illumina HiSeq 4000 at a targeted depth of 36 Mreads/sample and paired-end read length of 81,8i,8i,81. The reads were trimmed for adapters with bcl2fastq v2.20.0, aligned to the mouse genome mm10 with STAR 2.7.0e, and a count matrix was assembled using the cellranger v4.0 curation of ENSEMBL annotations. In the manuscript, “Gene expression” refers to natural logarithm of counts per million for bulk RNA-seq data. The data were collected from four independent experiments.

Single-cell RNA-seq of EpiTS embryoids (formed from 100ESC/100TSC condition) was performed with 10× single-cell 3’ gene expression reagent kit chemistry v3.1, according to the protocol CG000204 Rev D. Library QC was performed on an Agilent TapeStation 4200, and sequencing was performed on Illumina HiSeq 4000, with a paired-end read length of 28, 8i, 110, targeting ~3000 cells and 300 Mreads per library (which included two replicates per condition, 4 timepoints, epithelialized and non-epithelialized embryoids, for a total of 16 libraries). Recovered cells were 3300 ± 900, and reads per cell after UMI collapse of 29,000 ± 4500 (average ± SD). The reads were trimmed for adapters and polyA with cutadapt⁶⁰ v2.1, and aligned to mm10 with cellranger 3.1. The count matrices were imported in R v3.6 with Seurat⁶¹ v3.1. Live cells were selected based on detection of more than 2000 genes, and mitochondrial gene content of 1.5–15%, and counts were normalized as natural logarithm of counts normalized to 10k per cell (referred to as “Gene expression” in the manuscript). A mini-analysis including dimensionality reduction by PCA based on centered and scaled most variable genes and cell-type annotation transfer from an in vivo atlas⁶² with scmap⁶³ was performed on individual datasets for the needs of doublet removal with DoubletFinder v2.0.3⁶⁴. After data filtering, all datasets were merged, variable genes, scaling and PCA repeated, and batch correction was then done with Harmony v1⁶⁵. A first Louvain clustering yielded clusters that were assigned to germ layers. UMAPs⁶⁶ were computed with uwot v0.1.5, first with 100 cells per cluster and spectral initialization, and then with all cells, initialized on the previous cluster centroids plus noise. The data were then split by germ layers, and a refined Louvain clustering and UMAP view was computed for each subset. Louvain clusters were finally assigned to cell types based on canonical markers. Custom code was used for visualizing cell-type proportions vs day and/or epithelialization, normalizing for heterogeneous dataset sizes to avoid bias. A further closeup was similarly performed on the neurons of the epiblast + ectoderm subset. Splicing data were estimated with velocyto⁶⁷ v0.17, and RNA velocity was computed with scVelo v0.2.1⁶⁸ in deterministic mode, using python v3.7.2 and scanpy v1.5⁶⁹.

Further information on research design is available in the Nature Research Reporting Summary linked to this article.