GeoMx

The GeoMx Digital Spatial Profiler enables high-plex spatial and molecular analysis of RNA and protein from tissue specimens on slides. Tissue samples can be either fresh frozen or FFPE. Tissue slides are stained with large panels of pre-mixed biological probes, each containing a unique, UV-cleavable DNA barcode. The regions of interest (ROIs) are selected based on whole slide 4-color fluorescent morphology staining. Using the morphology markers for guidance, ROIs are illuminated with UV light to cleave the barcodes. The collected barcodes are then quantified using Illumina sequencer or the nCounter Analysis System (not available in our facility). Protein panels allow analyzing up to 96 different proteins and RNA up to the whole transcriptome.

The protocol includes three main parts, namely:

     A. Sample preparation and staining
     B. The proper DSP analysis that takes place in the GeoMx instrument, including ROI selection.
     C. The downstream quantification steps, either by nCounter or by NGS library construction and sequencing.

The detailed protocols, tutorials, and other material are available at NanoString University (https://www.nanostring.com/support/nanostring-university/). If you work at Tampere University and want to carry out the experiment by yourself, we highly recommend you to learn the steps in the protocol from Nanostring University. A core representative will help and supervise you during your first sample run. If you are affiliated outside Tampere University or want to carry out the experiment as a service due other reasons, your experiments will be run by the facility personnel for parts (A) and (B) (at an agreed cost) as a service and you will be able to select your ROIs remotely (B). After that, the collection plate will be sent to you for the downstream part (C).

You can find more information about the technique from here.
More information on the available panels: Protein or RNA

We recommend new users to contact NanoString’s Account Manager Reija Laitinen (rlaitinen(at)nanostring.com) and the technical support team (geomxsupport(at)nanostring.com) to discuss about their project and get help in choosing the most suitable experimental setup and reagents for them. 

Sample requirements:

• FFPE or Fresh/Frozen tissue
• Species Specific – only human and mouse samples currently supported
• Recommended section thickness is 5 µm
• Tissue should be sectioned onto positively charged slides no more than 2 weeks prior to your DSP experiment. 
  • Recommended slides: Leica Bond Plus (Cat# S21.2113.A) and Fisherbrand Superfrost Plus (Cat # 12-550-15)
• A test slide for a scanning only run (without ROI definition, UV illumination, or ROI collection) is strongly recommended to validate the fluorescent staining of your morphology markers. All requests utilizing custom antibodies are required to undergo this process.
• Multiple sections or sections from multiple tissues can be placed on the same slide for DSP processing. All sections on the slide must fit within the GeoMx gasket. The gasket dimensions are shown below.

Morphology marker selection:

Morphology markers are employed to guide selection of ROIs based on visual staining patterns. nanoString provides morphology kits that contain common tissue markers. Custom antibodies are also supported as long as the antibody conjugate works with one of the 4 channels on the instrument. We have a list of antibodies previously validated by the nanoString Technology Access Program. One of the fluorescent channels needs to be reserved for a nuclear stain, leaving three channels open for antibodies of interest. The list of available fluorescent channels are: