The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability
Open accessAbstract
Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification approach that uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide. The gene-specific probes are unlabelled and can therefore be synthesized at low cost, thus allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency. smiFISH is also flexible since differently labelled secondary detector probes can be used with the same primary probes. We demonstrate that this flexibility allows multicolor labelling without the need to synthesize new probe sets. We further demonstrate that the use of a specific acrydite detector oligonucleotide allows smiFISH to be combined with expansion microscopy, enabling the resolution of transcripts in 3D below the diffraction limit on a standard microscope. Lastly, we provide improved, fully automated software tools from probe-design to quantitative analysis of smFISH images. In short, we provide a complete workflow to obtain automatically counts of individual RNA molecules in single cells.
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Cites
Spatially resolved, highly multiplexed RNA profiling in single cells
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Self-citationVisualization of Single RNA Transcripts in Situ
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Analysis of focus measure operators for shape-from-focus
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In the right place at the right time: visualizing and understanding mRNA localization
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BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals
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Spatially resolved transcriptomics and beyond
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Cited by
P-Body Purification Reveals the Condensation of Repressed mRNA Regulons
Hubstenberger, A., Courel, M., Bénard, M., Souquere, S., Ernoult-Lange, M., Chouaib, R., Yi, Z., Morlot, J.-B., Munier, A., Fradet, M., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.003 · Cited by 787
Self-citationThe promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
Lein, E., Borm, L. E., & Linnarsson, S. (2017) · Science · doi:10.1126/science.aan6827 · Cited by 383
Moffitt, J. R., Hao, J., Bambah-Mukku, D., Lu, T., Dulac, C., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617699113 · Cited by 308
Tian, T., Shu, B., Jiang, Y., Ye, M., Liu, L., Guo, Z., Han, Z., Wang, Z., & Zhou, X. (2021) · ACS Nano · doi:10.1021/acsnano.0c08165 · Cited by 328
Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy
Wang, G., Moffitt, J. R., & Zhuang, X. (2018) · Scientific Reports · doi:10.1038/s41598-018-22297-7 · Cited by 256
Metadata
- Authors
- Tsanov, N., Samacoits, A., Chouaib, R., Traboulsi, A.-M., Gostan, T., Weber, C., Zimmer, C., Zibara, K., Walter, T., Peter, M., Bertrand, E., & Mueller, F.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-09-05
- Volume
- 44
- Issue
- 22
- Pages
- e165-e165
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2513030033
- Cited by
- 447
- References
- 25
- FWCI
- 13.57
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tsanov, N., Samacoits, A., Chouaib, R., Traboulsi, A.-M., Gostan, T., Weber, C., Zimmer, C., Zibara, K., Walter, T., Peter, M., Bertrand, E., & Mueller, F. (2016). smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Research. https://doi.org/10.1093/nar/gkw784
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