Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Methods Mol Biol. 2025;2856:419-432. doi: 10.1007/978-1-0716-4136-1_24.
Imaging-based spatial multi-omics technologies facilitate the analysis of higher-order genomic structures, gene transcription, and the localization of proteins and posttranslational modifications (PTMs) at the single-allele level, thereby enabling detailed observations of biological phenomena, including transcription machinery within cells and tissues. This chapter details the principles of such technologies, with a focus on DNA/RNA/immunofluorescence (IF) sequential fluorescence in situ hybridization (seqFISH). A comprehensive step-by-step protocol for image analysis is provided, covering image preprocessing, spot detection, and data visualization. For practical application, complete Jupyter Notebook codes are made available on GitHub ( https://github.com/Ochiai-Lab/seqFISH_analysis ).
基于成像的空间多组学技术有助于分析更高阶的基因组结构、基因转录以及在单等位基因水平上定位蛋白质和翻译后修饰 (PTMs)，从而能够详细观察生物现象，包括细胞和组织内的转录机制。本章详细介绍了这些技术的原理，重点介绍了 DNA/RNA/免疫荧光 (IF) 顺序荧光原位杂交 (seqFISH)。提供了一个全面的分步图像分析协议，涵盖了图像预处理、斑点检测和数据可视化。对于实际应用，完整的 Jupyter Notebook 代码可在 GitHub 上获得 ( https://github.com/Ochiai-Lab/seqFISH_analysis )。
