Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH.
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH.
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DOI：
10.1038/s41587-022-01455-3
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发表时间：
2023-02
影响因子：
46.9
通讯作者：
Linnarsson, Sten
中科院分区：
文献类型：
--
作者：
Borm, Lars E.;Albiach, Alejandro Mossi;Mannens, Camiel C. A.;Janusauskas, Jokubas;Ozgun, Ceren;Fernandez-Garcia, David;Hodge, Rebecca;Castillo, Francisca;Hedin, Charlotte R. H.;Villablanca, Eduardo J.;Uhlen, Per;Lein, Ed S.;Codeluppi, Simone;Linnarsson, Sten
对转录组进行空间分析的方法主要取决于分辨率和吞吐量之间的权衡。在这里，我们开发了一种名为增强型电子荧光原位杂交(EELFISH)的方法，它可以在不影响空间分辨率的情况下快速处理大组织样本。通过将RNA从组织切片电泳法转移到捕获表面，鳗鱼通过减少所需的成像量来加快数据采集速度，同时确保RNA分子直接向表面移动，保持单细胞分辨率。我们将鳗鱼应用于小鼠大脑的八个完整的矢状面，并测量了多达440个基因的表达模式，以揭示复杂的组织结构。此外，鳗鱼可以通过去除自体荧光脂褐素来研究具有挑战性的人类样本，使人类视觉皮质的空间转录组得以可视化。我们为仪器控制、图像处理、数据分析和可视化提供完整的硬件规格、所有协议和完整的软件。鳗鱼在大而复杂的组织样本中描述了单细胞的空间转录。
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. EEL FISH profiles spatial transcriptomes in single cells in large, complex tissue samples.
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影响因子：
48
作者：
Hershberg EA;Camplisson CK;Close JL;Attar S;Chern R;Liu Y;Akilesh S;Nicovich PR;Beliveau BJ
通讯作者：
Beliveau BJ
影响因子：
48
作者：
Biancalani T;Scalia G;Buffoni L;Avasthi R;Lu Z;Sanger A;Tokcan N;Vanderburg CR;Segerstolpe Å;Zhang M;Avraham-Davidi I;Vickovic S;Nitzan M;Ma S;Subramanian A;Lipinski M;Buenrostro J;Brown NB;Fanelli D;Zhuang X;Macosko EZ;Regev A
通讯作者：
Regev A
影响因子：
3.4
作者：
Aitken, Colin Echeverria;Marshall, R. Andrew;Puglisi, Joseph D.
通讯作者：
Puglisi, Joseph D.
影响因子：
56.9
作者：
Femino, A;Fay, FS;Singer, RH
通讯作者：
Singer, RH
影响因子：
64.5
作者：
Cho CS;Xi J;Si Y;Park SR;Hsu JE;Kim M;Jun G;Kang HM;Lee JH
通讯作者：
Lee JH