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Additional file 4:. Table S1. Gene sets down-regulated in dormant residual tumor cells. Clusters of SP-PIR Keywords identified by DAVID functional ontology analysis of genes down-regulated in dormant residual tumor cells compared to all other cell types (false discovery rate (FDR) 1.5-fold).

Additional file 5: Figure S4. Analysis of gene expression data for mitosis-related genes and mTOR pathway activity. (a, b) Expression of all differentially expressed cyclins and cyclin-dependent kinases in HER2/neu (a) and Wnt1 (b) models. (c) Relative expression of all ribosomal proteins, and unsupervised hierarchical clustering for HER2/neu (left) and Wnt1 (right) tumors. (d) Expression of mTOR signature in primary tumor (PT), residual lesion (RL), recurrent tumor (RT) and recurrent tumor stromal cells (RS), for individual (circles) and mean (black line) of pathway activity for HER2/neu (left) and Wnt1 (right) tumors. p-value vs. RL for mTOR signature of HER2/neu: PT

Additional file 7: Figure S5. HER2/neu-Prim1 residual disease is enriched for mesenchymal tumor cells. (a-c) IF staining for Hoechst 33258 (blue) and H2B-eGFP (green) along with luminal epithelial marker CK8 (red, top) or myoepithelial marker CK14 (red, bottom), on sections of H2B-eGFP-labeled orthotopic HER2/neu-Prim1 (a) or Wnt1-Prim1 (b) primary tumor (left), residual lesion 28 d after doxycycline withdrawal (right), or normal mammary gland (c). (d-g) Flow cytometry for CD49e vs. CD24 (d, e) or PDGFR-β vs. CD24 (f, g) on H2B-eGFP+DAPI- tumor cells from orthotopic H2B-eGFP-labeled orthotopic HER2/neu-Prim1 primary tumors (d, f) or MRLs (e, g). Scale bars 200 μm for all images.

Additional file 8: Figure S6. HER2/neu-Prim1 residual tumor cells do not express luminal or myoepithelial markers. (a-p) IF staining for Hoechst 33258 (blue) and H2B-eGFP (green) along with epithelial markers (red) CK5 (a, i), CK18 (b, j), CK19 (c, k), EpCAM (e, m), E-Cadherin (f, n), P-Cadherin (g, o), and p63 (h, p), or with a Pan-CK antibody (d, l), on sections of MRLs from H2B-eGFP-labeled orthotopic HER2/neu-Prim1 tumors (a-h) or normal mammary ducts (i-p). Scale bar 50 μm for all images.

Additional file 11: Table S5. TIC Frequency for Tumor Cells from H2B-eGFP-labeled Orthotopic HER2/neu-Prim1 Primary Tumors or Residual Lesions. Calculation of TIC frequencies for GFP + CD45-DAPI- singlet tumor cells from H2B-eGFP-labeled HER2/neu-Prim1 primary tumors or residual lesions, injected into nu/nu mice either on (HER2/neu transgene expressed), or not on (HER2/neu transgene not expressed), doxycycline.

Additional file 3 CD31 co-localizes with intravenously injected lectin-AF647. (a-f) Fluorescence microscopy for Hoechst 33258 (blue, a), IF for CD31 (red, b), H2B-eGFP (Green, d), lectin-AF647 (Yellow, eE), merge of CD31 and Lectin-AF647 (c), or merge of all channels (f) on H2B-eGFP-labeled orthotopic HER2/neu-Prim1 MRL. Scale bar 100 μm for all images.

Additional file 2: Figure S2. ECM protein expression in minimal residual lesions. (a-d) IF staining showing Hoechst 33258 (blue), H2B-eGFP (green) and either collagen type-I (red, a, c) or fibronectin (red, b, d) on H2B-eGFP-labeled orthotopic HER2/neu-Prim1 MRLs (a, b) or normal mammary ducts (c, d), labeled to show duct epithelial cells (D), or lumen (Lu). Scale bar 50 μm for all images.

Additional file 6:. Table S2. Gene sets up-regulated in dormant residual tumor cells. Clusters of SP-PIR Keywords identified by DAVID functional ontology analysis of genes up-regulated in dormant residual tumor cells compared to all other cell types (FDR 1.5-fold).

Additional file 9: Table S3. TIC frequency for syngeneic orthotopic MTB;TetO-HER2/neu;TTC;rYFP primary tumors and residual lesions. Calculation of TIC frequencies for YFP+ CD45-DAPI- singlet tumor cells from syngeneic orthotopic primary tumors or residual lesions in nu/nu mice generated from the same MTB;TetO-HER2/neu;TTC;rYFP donor tumors, injected into nu/nu mice on doxycycline.