Additional file 1: of AKT1low quiescent cancer cells persist after neoadjuvant chemotherapy in triple negative breast cancer

S2 Antibody target specificity is unaffected by sequence of primary antibody application. Merged (right) and single color (left) confocal microscopy images at × 60 of an untreated primary TNBC tumor stained in an alternate sequence: pan-AKT ➔ H3K9me2 ➔ HES1 (c.f. standard sequence of H3K9me2 ➔ pan-AKT ➔ HES1) demonstrating consistent cytoplasmic pan-AKT (green) and HES1 (red) staining and nuclear H3K9me2 (yellow) staining in an example QCC (white arrows). (PDF 3624 kb

Additional file 2: of AKT1low quiescent cancer cells persist after neoadjuvant chemotherapy in triple negative breast cancer

S1 Determination of fluorescence intensity thresholds and staining reproducibility. For each marker (HES1, H3K9me2, pan-AKT) the proportion of cells at a specific fluorescence intensity level was different between sequential sections from control tumor 4, stained simultaneously (S1A and S1B, respectively). QCC percentage (red bars) and QCC density (box and whisker plots) in control tumors 1–4 increased proportionally at 25%, 33%, and 50% thresholds (S1C, S1D, and S1E, respectively). (PDF 2666 kb