Membraneslide 1.0 pen slides

Nine pairs of STIC and normal tubal epithelium formalin-fixed and paraffin-embedded (FFPE) samples were retrieved from Johns Hopkins Hospital under institutional review boards approval and reviewed by pathologists. The diagnostic criteria for STIC was based on morphological and immunohistochemical criteria previously described (30 (link),31 (link)). The purity of each sample was estimated according to the proportion of STIC epithelial (p53+-staining) cells among total dissected epithelial cells including STIC and adjacent normal. For some samples, we intentionally dissected the STIC lesion with adjacent normal tubal epithelium in order to obtain enough DNA quantity for both methylomic and sequencing analysis. Another 12 frozen fallopian tube tissue samples were also retrieved and processed as FFPE sample and confirmed as normal tubal epithelium by H&E and p53 immunohistochemical stains. Details for each patient and sample are listed in Supplementary Table S8. All STIC and normal tubal samples were sectioned on the MembraneSlide 1.0 PEN slides (Zeiss) for laser capture micro-dissection (Leica LMD7000) of STIC and its adjacent normal epithelium. Genomic DNA was purified by using the QIAamp FFPE DNA tissue kit (Qiagen, Hilden, Germany).

MembraneSlide 1.0 PEN slides (Zeiss) were exposed to UV light for 30 min before mounting 8 μm sections. These slides were baked at 37°C for 30 min, then dewaxed for 5 min and rehydrated through graded alcohols to water for 3–5 min each. The slides were then briefly dipped in methyl green, washed in water and dried at 37°C for 1 h. Laser capture microdissection was performed with the laser capture PALM system (Zeiss). DNA was extracted using the PicoPure DNA extraction kit (Arcturus).