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Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

Eng, Chee-Huat Linus and Lawson, Michael and Zhu, Qian and Dries, Ruben and Koulena, Noushin and Takei, Yodai and Yun, Jina and Cronin, Christopher and Karp, Christoph and Yuan, Guo-Cheng and Cai, Long (2019) Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature, 568 (7751). pp. 235-239. ISSN 0028-0836. PMCID PMC6544023. doi:10.1038/s41586-019-1049-y. https://resolver.caltech.edu/CaltechAUTHORS:20190129-144119260

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Abstract

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells. Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells—with high accuracy and sub-diffraction-limit resolution—in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand–receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41586-019-1049-yDOIArticle
https://rdcu.be/bsQOyPublisherFree ReadCube access
https://github.com/CaiGroup/seqFISH-PLUSRelated ItemData
https://resolver.caltech.edu/CaltechAUTHORS:20210120-154339392Related ItemConference Abstract
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544023PubMed CentralArticle
ORCID:
AuthorORCID
Lawson, Michael0000-0002-2868-733X
Koulena, Noushin0000-0002-9419-5712
Yuan, Guo-Cheng0000-0002-2283-4714
Cai, Long0000-0002-7154-5361
Additional Information:© 2019 Springer Nature Publishing AG. Received 05 November 2018; Accepted 27 February 2019; Published 25 March 2019. Code availability: The custom written scripts used in this study are available at https://github.com/CaiGroup/seqFISH-PLUS. Data availability: RNA-seq data were obtained from GEO accession number GSE98674. RNA SPOTs data were obtained from a previous study. Source data from this study are available at https://github.com/CaiGroup/seqFISH-PLUS. All data obtained during this study are available from the corresponding author upon reasonable request. We thank L. Sanchez-Guardado from the Lois laboratory and the Thanos laboratory for providing mouse samples; S. Schindler for sectioning the tissue slices; J. Thomassie for help with data analysis; S. Shah for help with image analysis and input on the manuscript; K. Frieda for advice on the manuscript and help with making figures; and M. Thomsons, S. Chen and C. Lois for discussions. This project is funded by NIH TR01 OD024686, NIH HubMAP UG3HL145609, Paul G. Allen Frontiers Foundation Discovery Center and a Chan-Zuckerberg Initiative pilot grant. Author Contributions: C.-H.L.E. and L.C. conceived the idea and designed experiments. C.-H.L.E. performed all the experiments. M.L. performed image analysis. C.-H.L.E., M.L., Q.Z., R.D. and L.C. performed data analysis. L.C. and G.-C.Y. supervised the analysis process. C.-H.L.E. and N.K. performed cell segmentation and generated the primary probes. Y.T. designed the readout probes. C.-H.L.E., Y.T. and J.Y. validated the readout probes. C.C. and C.K. built the automated fluidic delivery system. C.-H.L.E., M.L, Q.Z., R.D. and Y.T. provided input for L.C. when writing the manuscript. L.C. supervised all aspects of the project. Competing interests: C.-H.L.E and L.C. filed a patent on the pseudocolour-encoding scheme in seqFISH+.
Funders:
Funding AgencyGrant Number
NIHTR01 OD024686
NIHUG3HL145609
Paul G. Allen Frontiers GroupUNSPECIFIED
Chan Zuckerberg InitiativeUNSPECIFIED
Subject Keywords:Genomics; Super-resolution microscopy
Issue or Number:7751
PubMed Central ID:PMC6544023
DOI:10.1038/s41586-019-1049-y
Record Number:CaltechAUTHORS:20190129-144119260
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190129-144119260
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92510
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:25 Mar 2019 16:58
Last Modified:09 Mar 2022 18:25

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