Digital spatial profiling (DSP) refers to the technology that allows for highly multiplexed protein or gene expression analysis within the two dimensional context of tissue architecture. Modern DSP platforms approach the resolution of single cell analysis, allowing for the elucidation of cellular heterogeneity within a tissue, organ, or disease process. There are two major spatial profiling platforms available in Duke CORE laboratories: the NanoString GeoMx and the 10x Genomics Visium. BRPC pathologists support Duke investigators’ DSP projects through experimental design suggestions, evaluation and identification of optimal tissues, and guidance with ROI selection.
Access to and use of the NanoString GeoMx Digital Spatial Profiler is available to any Duke investigator through the BRPC. The GeoMx DSP is housed within the BRPC laboratory space where all wet laboratory functions are performed, including tissue processing, slide cutting, slide staining, region of interest (ROI) selection, and oligonucleotide tag capture. Capture plates are then transported to other core laboratories for hybridization and detection on the nCounter instrument (for protein experiments) or for library preparation and next generation sequencing (for cancer transcriptome or whole transcriptome experiments). For protein expression experiments, the oligonucleotide tags with their quantitative counts are imported back into the GeoMx platform for integration with the slide images and ROI selections for quantitative spatially-resolved protein expression analysis. For transcriptome experiments, the 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. After sequencing, the FASTQ files are processed and converted to Digital Count Conversion (DCC) files on a dedicated server in the BRPC using the Nanostring GeoMx bioinformatics pipeline. The DCC files are then imported back into the GeoMx machine for investigator analysis. Investigators then have the option to access the GeoMx remotely to analyze their data using the NanoString Analysis Software Suite, or they can extract their data to analyze using their statistical software of choice. If additional biostatistics support is needed, investigators are referred to the Bioinformatics Service Center or the Genomic Analysis and Bioinformatics Core Facility, depending on whether their project is cancer-related or non-cancer-related.
Access to and use of the 10x Genomics Visium is available to any Duke investigator through the Molecular Genomics Core facility. The BRPC supports Visium experiments through tissue selection/evaluation, histology quality control, RNA quality control, and slide preparation. To learn more about the 10x Genomics Visium, click here.
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