PT  - JOURNAL ARTICLE
AU  - Lars E. Borm
AU  - Alejandro Mossi Albiach
AU  - Camiel C.A. Mannens
AU  - Jokubas Janusauskas
AU  - Ceren Özgün
AU  - David Fernández-García
AU  - Rebecca Hodge
AU  - Ed S. Lein
AU  - Simone Codeluppi
AU  - Sten Linnarsson
TI  - Scalable <em>in situ</em> single-cell profiling by electrophoretic capture of mRNA
AID  - 10.1101/2022.01.12.476082
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.12.476082
4099  - http://biorxiv.org/content/early/2022/01/13/2022.01.12.476082.short
4100  - http://biorxiv.org/content/early/2022/01/13/2022.01.12.476082.full
AB  - Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here, we developed a method named 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 towards the surface, preserving single-cell resolution. We applied EEL on eight entire sagittal sections of the mouse brain and measured the expression patterns of up to 440 genes to reveal complex tissue organisation. Moreover, EEL enabled the study of challenging human samples by removing autofluorescent lipofuscin, so that we could study the spatial transcriptome of the human visual cortex. We provide full hardware specification, all protocols and complete software for instrument control, image processing, data analysis and visualization.Competing Interest StatementThe authors declare the following competing interests: L.E.B., A.M.A., C.M., J.J., D.F.G., S.C. and S.L. are shareholders in EEL Transcriptomics AB, which owns intellectual property rights to the EEL method, including a patent application with L.E.B., S.C. and S.L. as co-inventors. S.L. is a paid scientific advisor to, and S.C. is a current employee of Rebus Biosystems, which has licensed the EEL intellectual property rights. The remaining authors declare no competing interests.