Joe Beechem on True Spatial Genomics using the GeoMx Digital Spatial Profiler

With the use of the GeoMx Digital Spatial Profiler (DSP) and the newly unveiled Spatial Molecular Imager (SMI), Joe Beechem, PhD discusses how spatial genomics research is expanding rapidly across various applications with multiple technologies.
0:30 History of genomics research
2:00 Limitations of bulk and single cell analysis
3:17 Three scales for understanding spatial biology
5:55 Overview of GeoMx Digital Spatial Profiler Technology
7:35 Workflow for using GeoMx Digital Spatial Profiler Technology
8:52 Compatible tissue samples compatible
9:23 Types of spatial profiling available
10:13 Use of micromirrors to obtain spatial resolution
11:35 Analysis of specific tissue structures
11:59 Application of GeoMx Digital Spatial Profiler in melanoma
14:07 Tools for examining RNA and protein from samples of interest
14:54 Fast timeline from experiment to publication
16:42 Research directions for translational cancer research using GeoMx Digital Spatial Profiler
17:09 Comparison of Nanostring technologies to FDA cleared assays
20:27 Reproducibility of RNA analysis with GeoMx Digital Spatial Profiler
21:06 RNA analysis with GeoMx Digital Spatial Profiler
22:35 Human and mouse whole transcriptome analysis
23:36 Application of whole transcriptome analysis to cancer research
24:40 Comparison of low, medium, and highly expressed genes
25:03 Application in colorectal cancer
25:50 Example of how whole transcriptome can change in space
27:18 Resolving differences in gene expression during tumor progression in colorectal cancer
28:45 Examination of whole transcriptomes at cellular boundaries
30:45 Solution to “lost in space” problem
32:49 Using RNA deconvolution to predict different cell types
33:25 Resolution at single cell and subcellular levels
34:50 History of Spatial Molecular Imager
36:06 Overview of automated Cyclic Imaging Chemistry
37:22 Typing and mapping cells with Spatial Molecular Imager
37:49 Number of genes needed for specific applications
38:31 Application of Spatial Molecular Imager in Melanoma
40:05 Using Spatial Molecular Imager to find rare T cells in kidney cancer
41:25 Application of Spatial Molecular Imager to CRISPR-Cas9 Screening
41:55 3D Mapping of individual RNAs in single cells
43:47 Summary of GeoMx Digital Spatial Profiler and Spatial Molecular Imager
44:57 Nanostring Product Development Roadmap
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PLEASE NOTE: The CosMx™ SMI instrument is not offered and/or delivered to the Federal Republic of Germany/for use in the Federal Republic of Germany for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof in a method used in fluorescence in situ hybridization for detecting a plurality of analytes in a sample without the consent of the President and Fellows of Harvard College (Harvard Corporation) as owner of the German part of EP 2 794 928 B1. The use for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof is prohibited without the consent of the President and Fellows of Harvard College (Harvard Corporation). The CosMx™ SMI decoder probes are not offered and/or delivered to the Federal Republic of Germany/for use in the Federal Republic of Germany for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof in a method used in fluorescence in situ hybridization for detecting a plurality of analytes in a sample without the consent of the President and Fellows of Harvard College (Harvard Corporation) as owner of the German part of EP 2 794 928 B1. The use for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof is prohibited without the consent of the President and Fellows of Harvard College (Harvard Corporation).

[@consiliumi1]

Amazing!

[@cegao1049]

Hi. It seems that after we put the slide(with thousands probes) into the SMI instrument, the reading out part is fully automatic?

[@jamiemoon7674]

Great video and product! Quick question for anyone to chime in- does GeoMx get sequences from all cells of an ROI or subsets specified by user (or based on staining)? Thank you

[@joseceja8783]

Hi Jamie, I think you can do both. You can either collect the entire ROI, or you can use the “Segmentation” function to collect specific segments within an ROI. For example, you can collect the tumor region (defined by PanCK Staining) in segment 1 of the ROI, and the Stromal region within the same ROI in Segment 2. I hope this helps.