GSM7928167: Patient 2 ROI 8 Stroma; Homo sapiens; OTHER
An FFPE section of HNSCC was deparaffinized and stained overnight with antibodies targeting cancer cells (PanCK), endothelial cells (CD31), and CAFs (FAP). The section was hybridized with the RNA probes before being loaded into the instrument. Regions of interests including four cell categories (PanCK+, CD31+, FAP+, PanCK-/CD31-/FAP-) were selected and segmented for collection and library preparation. Sample processing and sequencing were performed by the Technology Access Program at NanoString. Probe measurements and quality control data were provided by NanoString. Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.