Jun 06, 2025

Public workspaceHuBMAP | CosMx® SMI Manual Slide Preparation for RNA Assays

DOI
https://dx.doi.org/10.17504/protocols.io.eq2lyqk9pvx9/v1
  • Arivarasan Karunamurthy1,
  • Jie Chen1,
  • HJ Park1
  • 1University of Pittsburgh Medical Center
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
    Tech. support email: [email protected]
Liz McDonough
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DOI: https://dx.doi.org/10.17504/protocols.io.eq2lyqk9pvx9/v1
External link: http://www.nanostring.com
Protocol Citation: Arivarasan Karunamurthy, Jie Chen, HJ Park 2025. HuBMAP | CosMx® SMI Manual Slide Preparation for RNA Assays. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lyqk9pvx9/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: June 06, 2025
Last Modified: June 06, 2025
Protocol Integer ID: 219747
Keywords: smi manual slide preparation for rna assay, cosmx smi platform, rna assay, deeper insights into the cell atlas, cell atlas, rna, smi manual slide preparation, cell interaction, visualization software, protein analyte, cell, situ hybridization chemistry, smi, situ hybridization
Funders Acknowledgements:
Multiscale, Multimodal Analysis of Skin and Spatial Cell Organization
Grant ID: 5U54AR081775-04
Disclaimer
This CosMx ‱ Spatial Molecular Imager (SMI) User Manual and its contents are the property of Bruker Spatial Biology, Inc. (“ Bruker” ), and are intended solely for use by Bruker customers, for the purpose of operating the CosMx SMI System. The CosMx SMI System (including both its software and hardware components), this User Manual, and any other documentation provided to you by Bruker in connection therewith, are subject to patents, copyright, trade secret rights and other intellectual property rights owned by, or licensed to, Bruker. No part of the software or hardware may be reproduced, transmitted,
transcribed, stored in a retrieval system, or translated into other languages without the prior written consent of Bruker. For a list of patents, see www.nanostring.com/company/patents.
Abstract
The CosMx SMI platform is an integrated system with cyclic in situ hybridization chemistry, a high-resolution
imaging readout instrument, and an interactive data analysis and visualization software. The CosMx SMI platform enables rapid quantification and visualization of more than 18,000 RNA and 64 protein analytes. This flexible spatial single-cell solution drives deeper insights into the cell atlas, cell-cell interaction, cellular processes, and biomarker discovery.
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