Spatial Biology is a new, rapidly-developing and incredibly-powerful field that integrates various -omics technologies with a physical tissue slice so that the distribution of very large numbers of probes (to different RNA transcripts or proteins) can be determined and analysed. Thanks to a Medical Research Council grant we have been able to acquire 2 instruments from Bruker-Nanostring which offer complementary methods, the CosMx and GeoMx. They may not look very impressive from the outside but "under the bonnet" they combine very sophisticated and automated fluidics and microfluidics systems with high quality fluorescence imaging and generate vast amounts of data.
Because the systems are so complicated, sample preparation is time consuming and complex, and reagent costs are very expensive (on the CosMx, about £5,000 per slide analysed!), BIU operates the instruments as a paid-for service, we do not let users run the systems for themselves. Please contact spatial@soton.ac.uk with any enquiries.
Bruker-Nanostring CosMx Spatial Molecular Imaging Platform
The CosMx SMI can map the transcription profile of 6,000 different genes or 64 different proteins in tissue slices on microscope slides in a single run with sub-cellular accuracy (with whole transcriptome analysis available in the near future). All the information is automatically generated on the instrument (a 2-slide run can take 2 weeks) and uploaded to a cloud-based system (AtoMx) for analysis.
Bruker-Nanostring GeoMx Digital Spatial Profiler
The GeoMx DSP platform can map the entire transcriptome and >570 protein targets on a region-of-interest (ROI) basis within tissue slices on microscope slides. Probes are then eluted from the ROI, collected and used to generate "libraries" that are sent away for sequencing.
10x Genomics Visium CytAssist
The 10x Genomics Visium Cytassist is used to transfer RNA from a tissue slice on a microscope slide onto a special Visium slide that has capture areas containing an array of unique, microscopic, barcoded spots on it, where the barcodes correspond to unique spatial locations within the source tissue. The Visium slide is then processed, off-instrument, to label the captured RNA with location-specific sequences, that are detected by downstream sequencing.
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