In each sample, we simultaneously imaged HER2 and ER mature and nascent transcripts at high magnification (100X objective) in at least 32 regions (range: 32-79) inside macroscopic tumor areas that a pathologist had previously marked in an adjacent hematoxylin-eosin (H&E) stained section (Figure 1B and Supplementary Table 2). The gene discussed is ERBB2; the disease is neoplasm.