Extended Data Fig. 4: Automated cell type annotation.
From: An atlas of rabbit development as a model for single-cell comparative genomics
a, SingleR predicted cell type annotations for each cell of the rabbit atlas (n = 146,133 cells), following training on the mouse atlas. Only a subset of predicted labels are annotated for visual clarity. Predicted labels for all cells are more easily visualized via the interactive web app, accessible at https://marionilab.github.io/RabbitGastrulation2022/. b) Normalised SingleR correlation scores for each rabbit cell against all possible mouse labels. Cells are ordered according to the label assigned by SingleR. The final annotated cell types are also displayed to show how the model predictions relate with those assigned after validation. c) Cells of the rabbit (top) and mouse (bottom) (Imaz-Rosshandler et al.23) datasets in a SAMap integrated UMAP embedding (n = 576,472 cells). Cells are coloured and annotated according to the cell type labels of each respective atlas. The rabbit (r) and mouse (m) label numberings refer to those in the legends of Fig. 2c and Extended Data Fig. 4a respectively. The full list of IDs can also be found in Supplementary Tables 3–7. Shortened labels for the rabbit extra-embryonic ectoderm cell types have also been added. rT = Trophoblast; rA1 = Amnion 1; rA2 = Amnion 2; rA3 = Amnion 3; rCY = Cytotrophoblast; rSP = SCT progenitors; rES = Early SCT. All panels depict rabbit cells integrated across all samples (N = 19 embryos). SingleR correlation scores and cell type predictions are provided in the source data, along with the integrated UMAP coordinates and final cell type annotations.
