TSS: Morphology driven spatial transcriptomics with Nanostring's GeoMx Digital Spatial Profiler

Seminar Abstract: The GeoMx DSP is a novel digital technology (proprietary to ‪@brukerspatial‬) that is based on multiplexed measurement of protein and nucleic acids and offers unparalleled levels of precision coupled with the ability to quantify 150+ proteins and over 18,000 RNA targets on a formalin-fixed, paraffin-embedded (FFPE) or a fresh frozen (FF) tissue section on a microscope slide. In contrast to the sequential analysis of multi-target immunohistochemistry (IHC) slides, the GeoMx DSP samples all protein and/or RNA analytes on a single slide. This not only shortens experiments and simplifies data analysis, but also provides a higher multiplexing capacity (18,000+ targets) all with spatial context from Formalin-Fixed, Paraffin-Embedded (FFPE) or fresh frozen (FF) tissue sections. Based on NanoString’s proprietary digital barcoding technology, the GeoMx DSP platform measures local protein levels, and can be combined with RNA expression, within heterogeneous tissue samples. Combining both multiplexed nucleic acid and protein on the same platform gives researchers the ability to spatially resolve RNA when suitable antibodies do not exist. The GeoMx DSP assay is performed on the GeoMx DSP platform which includes imaging and fluidic components to capture spatial context, and current nCounter® or next-generation sequencing (NGS) instruments provide the quantification. Chapters: 0:00 – Welcome and Introduction to the NanoString Team 1:11 – About Nanostring 3:07 – GeoMx Digital Spatial Profiler Workflows & Capabilities 19:19 – Case Study: Single Cell Programs of Immune Activation in Human MSI vs MSS Colorectal Carcinoma 22:00 – Case Study: Spatiotemporal Analysis of Ischemic Stroke Transcript Profiles 25:35 – Case Study: Spatial Analysis of Neural Cell Proteomic Profiles following Ischemic Stroke in Mice using High-Plex Digital Spatial Profiling 26:39 – Case Study: Spatial Whole Transcriptome Profiling of Mouse Development with GeoMx WTA 29:00 – Case Study: Isolating the Heterogeneity of SARS-CoV-2 Lung Infection 37:36 – CosMx Spatial Molecular Imager 39:48 – Q&A To learn more about NanoString: GeoMx Digital Spatial Profiler – https://nanostring.com/products/geomx... nCounter Analysis System – https://nanostring.com/products/ncoun... CosMx Spatial Molecular Imager – https://nanostring.com/products/cosmx... -------------------------------------------------- For more information on upcoming MaGIC seminars: https://bioinformagic.io/events Follow MaGIC for more content: Twitter:   / magic_analytics   Instagram:   / magic_analytics   #bioinformatics #transcriptomics #proteomics #nanostring #geomx