GSM9027003: bph_bpn_bpniv_bpnlv_2023_033; Mus musculus; OTHER
3-5 um tissue sectioned were stained with RNAscope probes and GeoMx DSP oligo-conjugated RNA detection probes. GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a UV-photocleavable linker. After selecting regions of interest (ROIs) on the GeoMx DSP, the DSP barcodes are UV-cleaved and collected. During library preparation, the DSP barcodes are tagged with their ROI location, then sequenced on an Illumina sequencer. Slides were exposed to an in situ hybridization (ISH) probe overnight at 37 degrees and conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a UV-photocleavable linker. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed and then imported back into the GeoMx DSP analysis software for integration with the slide images and ROI selections for spatially-resolved RNA expression.