Figure 1.

Whole-embryo Tet mutants display morphological and molecular gastrulation defects

(A) Graphic view of the experimental design. Fluorescently tagged mESCs were injected into 4N or 2N blastocysts to generate whole-embryo or mixed chimeric embryos, which were subsequently index-sorted for scRNA-seq. For each embryo, the transcriptome was compared to a reference WT gastrulation atlas to see if injected cells introduce cell state, composition, and differentiation rate (temporal) changes.

(B) Representative images of E7.5–E9.5 Tet-TKO whole-embryo mutants generated by injection of Tet-TKO mESCs into 4N blastocysts. Dashed lines depict embryo structure. Arrowheads show aberrant accumulation of cells inside amniotic cavity. A, anterior; P, posterior; Al, allantois; Em, embryonic tissues. Scale bars, 100 μm.

(C) 2D-projection of transcriptome profiles of 7,480 control and 9,793 Tet-TKO cells from E7.5 to E8.5 whole-embryo chimeras onto the WT atlas. Major lineages of the WT atlas are highlighted on enlarged subpanels.

(D) Cell-type composition per embryo. Embryos (represented by columns) are arranged according to their inferred E_t on the x axis.

(E) Fraction of major lineages per embryo. Black and red dots represent control and Tet-TKO whole-embryo chimeras, respectively. Black line represents the moving average frequency of WT atlas embryos for each lineage, and the shaded gray area represents two moving standard deviations around the mean (window size = 9). Two-sided Wilcoxon-Mann-Whitney rank sum test was used to compare cell-type frequencies of the 11 control and 6 Tet-TKO embryos older than E_t = 7.5.

(F) Distribution of E_t between 16 control and 15 Tet-TKO whole-embryo chimeras sampled at E7.5. Wilcoxon-Mann-Whitney test, two-tailed. Data are represented as mean ± SD.

(G) Variance and mean single-cell time distributions of Tet-TKO and control whole-embryo chimeras. Black line represents the moving average variance of WT atlas embryos, and the shaded gray area represents two moving standard deviations around the mean (window size = 17).

See also Figures S1 and S2.