Journal: STAR Protocols

Article Title: Protocol for spatial analysis of multiple markers across adjacent tissue sections captured by RNAscope using CellProfiler

doi: 10.1016/j.xpro.2025.103914

Figure Lengend Snippet: Modular pipeline architecture organized by functional category (A) ROI image data input and signal enhancement modules for importing and enhancing RNAscope ROI images; (B) Object identification modules for qualitative and quantitative assessments of nuclear, cytoplasmic, and extracellular localizations with their respective markers; (C) Filtering and classification modules for cell typing and intermarker association quantification; (D) Neighborhood analysis modules for evaluating intermarker associations and marker density; (E) Measurement and visualization modules for spatial and tissue profile assessment. Static modules (gray) required minimal adjustment across tissue types. Variable modules (blue) are slide- and/or tissue-specific, requiring additional customization for specific gene or intermarker associations.

Article Snippet: Scan and visualize RNAscope slides using a pathology imaging system (e.g., Vectra Polaris Automated Quantitative Pathology Imaging System [Akoya Biosciences, Perkin Elmer]), as discussed by Sari et al . 4.

Techniques: Functional Assay, RNAscope, Marker

Journal: Scientific Reports

Article Title: An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data

doi: 10.1038/s41598-024-58641-3

Figure Lengend Snippet: RNAScope targets and detection specifications.

Article Snippet: Commercial RNAScope control slides containing mouse NIH 3T3 cells (Advanced Cell Diagnostics, US) were used as a positive control sample for RNAScope for all samples.

Techniques: RNAscope

Journal: bioRxiv

Article Title: FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data

doi: 10.1101/2023.06.28.546871

Figure Lengend Snippet:

Article Snippet: Commercial RNAScope control slides containing mouse NIH 3T3 cells (Advanced Cell Diagnostics, US) were used as a positive control sample for RNAScope for all samples.

Techniques:

Journal: bioRxiv

Article Title: A new method for the sampling and preservation of placental specimens in low-resource settings for histology and analysis of nucleic acids

doi: 10.1101/2022.01.12.476059

Figure Lengend Snippet: RNAscope ® hybridization with probes for three genes. A . DAPI B . MEG3 C . ERVW-1 D . DIO3OS. E . Merged. Scale bar is 20 μm.

Article Snippet: RNAscope slides were imaged on a Zeiss Apotome microscope.

Techniques: Hybridization