Extended Data Fig. 1: Model description, Enrichr analysis, FACS controls and MMTV-HER2 scRNASeq data distribution.

(a) Experimental design of MMTV-HER2 bulk and single-cell RNA sequencing experiments. (b) Enrichr analysis^30,31 of differentially expressed genes (DEG) in MMTV-HER2 early lesion (EL) and primary tumor (PT) 7-day spheres bulk RNAseq. Full table in Supplementary Table 2. Orange, terms mentioned in the text. (c) Biological negative controls used for FACS gating strategy. FvB mammary gland (MG) was used to set the MMTV-HER2 EL and PT gate and FvB lungs for MMTV-HER2 eL and LL DCCs (see Fig. 1f). (d) Number of cells per cluster analyzed in the single-cell RNAseq of MMTV-HER2 EL (teal), PT (red), eL (early lungs, blue) and LL (late lungs, orange) DCCs (see Fig. 1d, e). (e) Number of UMIs per cluster (left) and per sample (right) analyzed in the single-cell RNAseq (see Fig. 1d, e). (f) Percentage of epithelial (EpCAM⁺Eng⁻), hybrid (EpCAM⁺Eng⁺) and mesenchymal (EpCAM⁻Eng⁺) populations in CD45⁻HER2⁺ MMTV-HER2 EL, PT and eL (early lungs) and LL (late lungs) DCCs after tissue dissociation (representative FACS plots in Fig. 1f). Graph shows n = 5 mice/condition, median, SEM and 2⁻tailed multiple t-tests.

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