Extended Data Fig. 10: The integrated Human Breast Cell Atlas (iHBCA) highlights effects of tissue preparation and confirms Milo differential abundance results.

(a) The global iHBCA uniform manifold approximation and projection (UMAP) plots coloured individually by each dataset (rest plotted underneath in grey). (b) Standard negative-binomial differential abundance analysis performed on the iHBCA for each of the comparisons previously explored using Milo on the Human Breast Cell Atlas (HBCA). Here we used the same base blocking terms as used in the milo analysis but with additional terms for dataset and live_sorting status (see Methods for details). (c) Global iHBCA UMAP showing the distribution of cells from fresh and frozen tissue. (d) Box and whisker plot showing the number of cells sequenced per individual across datasets. Donor numbers: Reed (n = 55), Nee (n = 22), Twigger (n = 18), Kumar (n = 126), Pal (n = 21), Gray (n = 16), Murrow (n = 28). The boxplot centers show median values while the minima / maxima show the 25th /75th percentiles respectively and whiskers extend to the most extreme datapoint within 1.5 × IQR (inter-quartile range) of the outer hinge of the boxplot. Outliers are then displayed independently.