ArticleNature protocols2017
mRNA quantification using single-molecule FISH in Drosophila embryos.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
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- Conserved RNA helicase Vasa regulates ribonucleoprotein condensate dynamics and mRNA localization.iScience · 2026Article
- FINDER converts zero-background kinetic fingerprinting into area-scalable attomolar biomarker detection.bioRxiv : the preprint server for biology · 2026Article
- NADThe EMBO journal · 2026Article
- Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering ofbioRxiv : the preprint server for biology · 2026Article
- Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses.The EMBO journal · 2026Article
- Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization.Nature communications · 2026Article
- Conserved RNA helicase Vasa regulates ribonucleoprotein condensates through protein interaction and mRNA recruitment.bioRxiv : the preprint server for biology · 2025Article
- Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development.Nature communications · 2025Article
- A conserved role for centriolar satellites in translation of centrosomal and ciliary proteins.The Journal of cell biology · 2025Article
- Abundant piRNA production mediated by theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The homie insulator has sub-elements with different insulating and long-range pairing properties.Genetics · 2025Article
- ThebioRxiv : the preprint server for biology · 2025Article
- RNA-Fluorescence In Situ Hybridization for the Detection of RNA in Mammalian Oocytes and Embryos.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Chromosome structure ineLife · 2024Article
- Article
- Direct observation of translational activation by a ribonucleoprotein granule.Nature cell biology · 2024Article
- Localization of RNAs to the mitochondria-mechanisms and functions.RNA (New York, N.Y.) · 2024Review
- Development of Aptamer-DNAzyme based metal-nucleic acid frameworks for gastric cancer therapy.Nature communications · 2024Article
- Spatial transcriptomic profiling of isolated microregions in tissue sections utilizing laser-induced forward transfer.PloS one · 2024Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.
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