Figure 1

FFPE material before and after punching. Hematoxylin and eosin-stained tissue sections and paraffin block of patient 4 are shown before and after punching tissue cores. Areas of IDC (red), DCIS (blue) and normal tissue (green) were marked on the original tissue section (A) and on the corresponding paraffin block (B). Tissue cores (E) were taken with a tissue microarrayer instrument. Thereafter, sections were made from the remaining block and a control staining and RNA isolation were done at ~400 μm intervals through the block (C and D). The area containing DCIS was lost after ~400 μm and tissue cores contained fat instead of tumor tissue. It was known from previous experiments that very little RNA can be isolated from fat cells. Therefore, expression measurements in tissue cores containing fat besides tumor tissue are not compromised.