The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
FISH-quant: automatic counting of transcripts in 3D FISH images
Open accessAbstract
Transcription is inherently stochastic even in clonal cell populations 1. Studies at single-cell-single-molecule level enable a quantitative understanding of the underlying regulatory mechanisms 2,3. A widely used technique is single-molecule RNA fluorescence in-situ hybridization (FISH), in which fluorescent probes target the mRNA of interest and individual molecules appear as bright diffraction-limited spots (Fig. 1a,b) 3. Recent experimental progress makes FISH easy to use 4 , but a dedicated image analysis tool is currently missing. Available methods allow counting of isolated mature mRNAs but cannot reliably quantify the dense mRNA aggregates at transcription sites (TS) in three dimensions (3D), particularly of highly transcribing genes 4. We developed FISH-QUANT to close this gap (Supplementary Note 1)
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Imaging individual mRNA molecules using multiple singly labeled probes
Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A., & Tyagi, S. (2008) · Nature Methods · doi:10.1038/nmeth.1253 · Cited by 2,028
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Zenklusen, D., Larson, D. R., & Singer, R. H. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1514 · Cited by 684
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Boireau, S., Maiuri, P., Basyuk, E., de la Mata, M., Knezevich, A., Pradet-Balade, B., Bäcker, V., Kornblihtt, A., Marcello, A., & Bertrand, E. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200706018 · Cited by 191
Self-citation
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Self-citationSingle-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
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Brett, J. O., Arjona, M., Ikeda, M., Quarta, M., de Morrée, A., Egner, I. M., Perandini, L. A., Ishak, H. D., Goshayeshi, A., Benjamin, D. I., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0190-0 · Cited by 162
Alternative polyadenylation of Pax3 controls muscle stem cell fate and muscle function
de Morree, A., Klein, J. D. D., Gan, Q., Farup, J., Urtasun, A., Kanugovi, A., Bilen, B., van Velthoven, C. T. J., Quarta, M., & Rando, T. A. (2019) · Science · doi:10.1126/science.aax1694 · Cited by 81
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Decoupled degradation and translation enables noise modulation by poly(A) tails
Grandi, C., Emmaneel, M., Nelissen, F. H. T., Roosenboom, L. W. M., Petrova, Y., Elzokla, O., & Hansen, M. M. K. (2024) · Cell Systems · doi:10.1016/j.cels.2024.05.004 · Cited by 8
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Lattanzio, M. V., Šoštarić, N., Kanagasabesan, N., Popović, B., Bradarić, A., Wardak, L., Guislain, A., Savakis, P., Tutucci, E., & Wolkers, M. C. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00592-0 · Cited by 3
Metadata
- Authors
- Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E., Darzacq, X., & Zimmer, C.
- Venue
- Nature Methods
- Published
- 2013-03-28
- Volume
- 10
- Issue
- 4
- Pages
- 277-278
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2077468928
- Cited by
- 366
- References
- 3
- FWCI
- 8.35
- Type
- journal article
- Language
- en
- Open access
- green
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