Extended Data Fig. 3. Quality control of joint embedding across single cell technologies.

a) Left panel: Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction showing joint embedding of WT (17,702 cells; n = 7 mice), Tet2 KO (18,651 cells; n = 7 mice), Dnmt3a KO (13,858 cells, n = 4 mice) and Idh2-R140Q (9,883 cells, n = 3 mice) lineage-negative hematopoietic progenitors. Right panels: UMAP embedding obtained for each scRNA-seq method is shown separately. b) Gene expression correlation between cells obtained by different scRNA-seq methods (Chromium v2, Chromium v3 and Drop-seq) that were mapped to the same cell cluster. The gene expression frequency was calculated as the number of unique molecular identifiers (UMIs) mapping to a given gene relative to the total number of UMIs detected for a given cluster, and multiplied by a factor of 10⁵. The log₂ of the pseudo-bulk gene expression is shown (R² values were obtained from Pearson correlation; red dots highlight the top gene markers for each cluster). c) Gene expression correlation between WT cells and expression profiles from the Mouse Cell Atlas⁶⁴ dataset, as obtained by scMCA⁶⁵ (see online methods).