瑞典卡罗林斯卡医学院Sten Linnarsson和Lars E. Borm共同合作近期取得重要工作进展，他们研究使用EEL FISH策略，通过电泳捕获mRNA进行可扩展的原位单细胞分析。这一研究成果于2022年9月22日在线发表于《自然—生物技术》杂志上。

研究人员开发了一种名为增强型电荧光原位杂交（EEL FISH）的方法，该方法可以在不影响空间分辨率的情况下快速处理大型组织样本。通过将组织切片中的RNA电泳转移到捕获表面上，EEL通过减少所需的成像量来加速数据采集，同时确保RNA分子直接向下移动到表面，从而保持单细胞分辨率。研究人员将EEL应用于小鼠大脑的八个完整矢状切面，并测量多达440个基因的表达模式，以揭示复杂的组织结构。

此外，EEL可用于通过去除自发荧光脂褐质来研究具有挑战性的人体样本，从而使人类视觉皮层的空间转录组可视化。研究人员提供了完整的硬件规格，所有的协议和用于仪器控制、图像处理、数据分析和可视化的完整软件。

据介绍，对转录组进行空间分析的方法主要是在分辨率和通量之间进行权衡。

附：英文原文

Title: Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH

Author: Borm, Lars E., Mossi Albiach, Alejandro, Mannens, Camiel C. A., Janusauskas, Jokubas, zgn, Ceren, Fernndez-Garca, David, Hodge, Rebecca, Castillo, Francisca, Hedin, Charlotte R. H., Villablanca, Eduardo J., Uhln, Per, Lein, Ed S., Codeluppi, Simone, Linnarsson, Sten

Issue&Volume: 2022-09-22

Abstract: Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here we develop a method named Enhanced ELectric Fluorescence in situ Hybridization (EEL FISH) that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down toward the surface, preserving single-cell resolution. We apply EEL on eight entire sagittal sections of the mouse brain and measure the expression patterns of up to 440 genes to reveal complex tissue organization. Moreover, EEL can be used to study challenging human samples by removing autofluorescent lipofuscin, enabling the spatial transcriptome of the human visual cortex to be visualized. We provide full hardware specifications, all protocols and complete software for instrument control, image processing, data analysis and visualization.

DOI: 10.1038/s41587-022-01455-3

Source: https://www.nature.com/articles/s41587-022-01455-3