GSM5123653: Phase II dysplastic nevus NS9 ROI1 [NS09-01]; Homo sapiens; OTHER
Following standard ISH protocols, samples were incubated with 1) DNA oligo-barcoded ISH probes containing a UV-photocleavable linker and 2) flourescently labeled antibodies for visualization of morphological structures. Areas of interest (AOI) within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x) Each collection of oligo tags from one well (representing an AOI 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. Concentration and purity of the resulting libraries was measured using a Bioanalyzer high-sensitivity DNA assay and Qubit high-sensitivity dsDNA kit.