The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy
Open accessAbstract
As an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging. Here we report an approach that combines MERFISH and expansion microscopy to substantially increase the total density of RNAs that can be measured. Using this approach, we demonstrate accurate identification and counting of RNAs, with a near 100% detection efficiency, in a ~130-RNA library composed of many high-abundance RNAs, the total density of which is more than 10 fold higher than previously reported. In parallel, we demonstrate the combination of MERFISH with immunofluorescence in expanded samples. These advances increase the versatility of MERFISH and will facilitate its application to a wide range of biological problems.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Spatially resolved, highly multiplexed RNA profiling in single cells
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969
Self-citationHell, S. W. (2007) · Science · doi:10.1126/science.1137395 · Cited by 2,967
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
Visualization of Single RNA Transcripts in Situ
Femino, A. M., Fay, F. S., Fogarty, K., & Singer, R. H. (1998) · Science · doi:10.1126/science.280.5363.585 · Cited by 1,504
Chen, F., Tillberg, P. W., & Boyden, E. S. (2015) · Science · doi:10.1126/science.1260088 · Cited by 1,501
Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells
Huang, B., Babcock, H., & Zhuang, X. (2010) · Cell · doi:10.1016/j.cell.2010.12.002 · Cited by 1,156
Self-citationMultiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT
Jungmann, R., Avendaño, M. S., Woehrstein, J. B., Dai, M., Shih, W. M., & Yin, P. (2014) · Nature Methods · doi:10.1038/nmeth.2835 · Cited by 1,128
Single-cell in situ RNA profiling by sequential hybridization
Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M., & Cai, L. (2014) · Nature Methods · doi:10.1038/nmeth.2892 · Cited by 985
Highly Multiplexed Subcellular RNA Sequencing in Situ
Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., et al. (2014) · Science · doi:10.1126/science.1250212 · Cited by 973
In situ sequencing for RNA analysis in preserved tissue and cells
Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C., & Nilsson, M. (2013) · Nature Methods · doi:10.1038/nmeth.2563 · Cited by 934
Cited by
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479
“, 2015], and spatial [Wang et al., 2018] data.”
RNA sequencing: the teenage years
Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 1,915
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH
Eng, C.-H. L., Lawson, M., Zhu, Q., Dries, R., Koulena, N., Takei, Y., Yun, J., Cronin, C., Karp, C., Yuan, G.-C., et al. (2019) · Nature · doi:10.1038/s41586-019-1049-y · Cited by 1,754
Exploring tissue architecture using spatial transcriptomics
Rao, A., Barkley, D., França, G. S., & Yanai, I. (2021) · Nature · doi:10.1038/s41586-021-03634-9 · Cited by 1,700
Metadata
- Authors
- Wang, G., Moffitt, J. R., & Zhuang, X.
- Venue
- Scientific Reports
- Published
- 2018-03-19
- Volume
- 8
- Issue
- 1
- Pages
- 4847-4847
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2785264903
- Cited by
- 256
- References
- 46
- FWCI
- 8.24
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. https://app.cochat.ai/papers/10.1038/s41598-018-22297-7
- The paper
- Wang, G., Moffitt, J. R., & Zhuang, X. (2018). Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Scientific Reports. https://doi.org/10.1038/s41598-018-22297-7
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
