Protocol for spatial analysis of multiple markers across adjacent tissue sections captured by RNAscope using CellProfiler
Issued Date
2025-09-19
Resource Type
eISSN
26661667
Scopus ID
2-s2.0-105008527705
Journal Title
STAR Protocols
Volume
6
Issue
3
Rights Holder(s)
SCOPUS
Bibliographic Citation
STAR Protocols Vol.6 No.3 (2025)
Suggested Citation
Copeland K., Permata Sari A.I., Copeland J., Jinawath N., Shiao M.S. Protocol for spatial analysis of multiple markers across adjacent tissue sections captured by RNAscope using CellProfiler. STAR Protocols Vol.6 No.3 (2025). doi:10.1016/j.xpro.2025.103914 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/110941
Title
Protocol for spatial analysis of multiple markers across adjacent tissue sections captured by RNAscope using CellProfiler
Corresponding Author(s)
Other Contributor(s)
Abstract
Here, we present a protocol for quantifying the expression of genes detected by fluorescence in situ hybridization at single-cell spatial resolution using an imaging analysis pipeline developed based on CellProfiler software. We describe steps for comparing gene expression between cancer samples with and without metastasis. We detail procedures for detecting target transcripts using RNAscope multiplex fluorescent assays and visualization using Vectra Polaris Automated Quantitative Pathology Imaging. This protocol also provides an alternative option to analyze signal interactions across adjacent tissue sections. For complete details on the use and execution of this protocol, please refer to Sari et al.<sup>1</sup>