Extended Data Fig. 8: Quality control of organoid scRNA-seq dataset.
From: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
a, UMAP (uniform manifold approximation and projection) of scRNA-seq data from all organoid samples. b, UMAP representations coloured by donor ID. The three donors correspond to E001, B044 and B080. c, Logistic regression probabilities. d, Experimental timeline for endometrial organoid cultures. Clonal organoids were derived in Expansion Medium (ExM) with CHIR99021 (CHIR) and ROCK inhibitor Y-22763 (Ri), grown in ExM and then subjected to hormonal stimulation with estrogen (E2) followed by E2 + progesterone (P4) + cyclic AMP (cAMP) and prolactin (PRL). The time points at which organoids were collected for scRNA-seq are shown with an asterisk. Representative bright field images of organoids for some of the timepoints are shown. e, UMAP projections of scRNA-seq data from two clonal organoids derived from the same individual. f, UMAP representations coloured by hormonal stimulation, cell cycle phase, individual clone, days after hormonal stimulation, sample ID. g, Dot plot showing log2-transformed expression of selected genes that distinguish the main cell populations. NH = No hormone; E2 = Estrogen; P4 = Progesterone; d = days.
