Aug 27, 2025

Public workspaceCarver et al, Aged Brain Spatial Profiling  - CosMx

DOI
https://dx.doi.org/10.17504/protocols.io.dm6gp3yb5vzp/v1
  • Chase Carver1
  • 1Mayo Clinic
  • Cellular Senescence Network (SenNet) Method Development Community
Chase Carver
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DOI: https://dx.doi.org/10.17504/protocols.io.dm6gp3yb5vzp/v1
Protocol Citation: Chase Carver 2025. Carver et al, Aged Brain Spatial Profiling - CosMx. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp3yb5vzp/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: October 04, 2023
Last Modified: August 27, 2025
Protocol Integer ID: 88813
Keywords: aged brain white matter, modifiable features of aged brain white matter, aged brain spatial profiling, nanostring cosmx platform, associated microglia, cosmx, cosmx this protocol, spatial molecular imaging, process for spatial molecular imaging
Funders Acknowledgements:
NIH Cellular Senescence Network
Grant ID: UG3 CA275669-01
Abstract
This protocol provides the process for spatial molecular imaging using the Nanostring CosMx platform used in
Carver et al., "Senescent- and disease-associated microglia are modifiable features of aged brain white matter".
Troubleshooting
CosMx Slide Preparation
Using FFPE sections, follow the protocol found in the document Download MAN-10159-02_CosMx_SMI_Manual_Slide_Preparation_Manual.pdfMAN-10159-02_CosMx_SMI_Manual_Slide_Preparation_Manual.pdf2.7MB

CosMx Instrument run
Follow the protocol found in the document Download MAN-10161-02-1_CosMx_SMI_Instrument_User_Manual.pdfMAN-10161-02-1_CosMx_SMI_Instrument_User_Manual.pdf1.8MB
for imaging of flow cells, FOV selection, and running spatial molecular imaging on the instrument.
The Cell Segmentation Profile used for mouse brain RNA is Configuration B. Cell overlay files are generated with the completion of the CosMx imaging and are used to segment 2D cell areas to be used in conjunction with transcript localization data.

Protocol references
MAN-10159-02_CosMx_SMI_Manual_Slide_Preparation_Manual