Digital Spatial Profiling (DSP) Core Facility

Welcome to the Department of Laboratory Medicine and Pathology (DLMP) Digital Spatial Profiling (DSP) core facility! We are happy to assist you in executing your spatial profiling experiments of RNA and protein in tissue sections on the NanoString GeoMx DSP platform. The facility is located in the E-building of the University of Washington’s South Lake Union (SLU) campus and is staffed by an experienced research scientist. The core facility is overseen by pathologists with hands-on experience executing DSP experiments. Read their recent publication using DSP on human kidney biopsies obtained in the clinic. The DSP core facility is located adjacent to the Pathology Research Services laboratory enabling seamless data generation from submitted tissues/tissue blocks.

Director: Shreeram Akilesh, MD PhD
Co-Director: Kelly D. Smith, MD PhD
Research Scientists: James Li, PhD, and Galen Stewart, BS

Why Perform Spatial Profiling?

Spatially resolved profiling of tissues was Nature Methods’ 2020 Method of the Year. Bulk profiling approaches such as RNA-seq lose information about the relative composition of the tissue. Even techniques which excel at identifying rare cell populations such as single cell RNA-seq, lose information about where in the tissue those cells are located. Spatial profiling enables deep phenotypic (protein/RNA) profiling and mapping of those profiles to specific locations within the tissue context. This is especially powerful when the processes under study are unevenly distributed in the tissue (e.g., patchy disease involvement).

Platform and Principle

Click image to enlarge. See detailed description of the flowchart. Source: NanoString Grant Support Package.

The NanoString GeoMx DSP permits direct quantification of proteins or RNA transcripts to spatially resolved anatomic structures in tissue sections. After hybridization of specially oligo-conjugated antibodies or RNA in situ hybridization (RNA-ISH) probes to a section, the tissue is counterstained and imaged using immunofluorescence microscopy. Structures of interest are visualized and selected as Regions of Interest (ROI). An ultraviolet laser pulse is focused precisely on this ROI to release oligos conjugated to the target proteins or RNAs. The DSP instrument aspirates these oligos into collection wells using a capillary micropipette. Since these oligos contain barcodes which map them to their source protein/RNA target, digital counting of these oligos with nCounter or next generation sequencing permits a direct readout of target abundance localized to the specific ROI within the tissue section. Read the original paper describing the technology. Read publications using the GeoMx DSP.

Sample Requirements

Only a single 4-6µm tissue section (fresh frozen and embedded in OCT or formalin fixed paraffin embedded, FFPE) is required for DSP data generation. If tissues are small, multiple tissues can be placed onto a single slide to reduce reagent costs and to achieve enough replicates for experiment interpretation (e.g., a tissue microarray). Samples must be placed within the green boxed area on a positively charged slide (see schematic). Tissue less than three years old is ideal, but older tissues have also been evaluated successfully. We recommend cutting tissue sections fresh for RNA analysis (within two weeks of the planned experiment; store sections at 4°C with desiccant). For protein assays, sections are stable at room temperature. We strongly recommend coordinating with us prior to cutting your tissue sections.

Source: NanoString manual.

Getting Started

Since DSP experiments are complex, we require an initial consultation so that we may assist you with planning and design of your experiment. Please contact us to schedule your consultation. For a one-time fee, we will discuss your project goals, sample type, desired analyte (protein/RNA), timeline and estimated cost. The major determinants of overall project cost will be the number of desired slides to be processed, region of interest (ROI) number and size, and nCounter/sequencing requirements. We are committed to working with you to execute your spatial profiling experiments efficiently and cost-effectively.

Grant Resources

Do you want to propose using the GeoMx DSP in your grant? Please find a comprehensive grant support package provided by NanoString. Specific information about the UW DLMP GeoMx DSP core facility will also be provided here shortly.

Additional Resources

Nanostring University
GeoMx DSP publications (>100 and growing!)
GeoMx DSP manual
GeoMx DSP white papers such as co-labeling with ACDBio RNAScope probes and many others