GSM9471513: Spatial profiling of a small cluster ROI from ovarian cancer patient BB24-011_2; Homo sapiens; OTHER
FFPE tissue sections were deparaffinized. Target retrieval was performed by incubating in Tris-EDTA at 99°C for 15 minutes. RNA targets were exposed by incubating with 1 μg/mL proteinase K at 37°C for 15 minutes. Samples were post-fixed and then incubated overnight with NanoString GeoMx Whole Transcriptome Atlas probes. Following probe hybridization, slides were washed and stained with SYTO83 (nuclear stain), anti-PanCK antibody, and anti-CLDN6 antibody for 100 minutes. Slides were scanned using the GeoMx Digital Spatial Profiler. Regions of interest (ROIs) were selected from CLDN6-positive/Pan-CK-positive areas. Barcoded oligo probes were collected from PanCK-positive segmented regions by UV-cleavage. The collected oligos were then indexed by PCR using the GeoMx Seq Code Pack to generate sequencing libraries.