Single cell in situ RNA profiling by sequential hybridization

By Eric Lubeck, A. Coşkun, T. Zhiyentayev, Mubhij Ahmad, Long Cai. Nature Methods, 2014

957 citations recorded by the source corpus.

In our previous paper, Lubeck and Cai, we used super-resolution microscopy to resolve a large number of mRNAs in single cells. In this Correspondence, we present a sequential barcoding scheme to multiplex different mRNAs.

Subfields: Biophysics, Media Technology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9bc923b60f93ce314e6db6449ac877693168c952

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Citations in the corpus

An introduction to spatial transcriptomics for biomedical research (2022, methodology): “seqFISH uses 4 fluorophores, with barcode length n depending on the number of genes targeted, to profile up to the whole genome in vitro [44].”
Best practices for single-cell analysis across modalities (2023, background): “Tangram 224 , GridNet 230 and eggplant 231 generate common coordinate frameworks across samples to mitigate this issue 232 .”
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics (2022, methodology): “Non-sequencing-based technologies, such as seqFISH 66 and MERFISH 67 , mostly rely on single-molecule fluorescence in situ hybridization (smFISH) and are directly of single-cell resolution.”
Giotto: a toolbox for integrative analysis and visualization of spatial expression data (2021, background): “Recently, a number of technological advances have enabled transcriptomic/proteomic profiling in a spatially resolved manner [3 – 14] such that cellular features (for example transcripts or proteins) can be assigned to single cells for which the original cell location information is retained (Fig.”
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression (2019, methodology): “In the sequential FISH approach using a color-coding scheme that requires each RNA molecule to be “on” in one of the several true color channels in each imaging round, as previously reported in seqFISH (49), increasing the number of hybridization rounds does not decrease the RNA spot density per rou”
The Human Cell Atlas (2017, neutral): “Techniques are being developed to assay: in situ gene expression in tissues at single-cell and even sub-cellular resolution (Chen et al., 2015b; Ke et al., 2013; Lee et al., 2014; Lubeck et al., 2014; Shah et al., 2016; Ståhl et al., 2016); the distribution of scores of proteins at cellular or sub-c”