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Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

Lohoff, T. and Ghazanfar, S. and Missarova, A. and Koulena, N. and Pierson, N. and Griffiths, J. A. and Bardot, E. S. and Eng, C.-H. L. and Tyser, R. C. V. and Argelaguet, R. and Guibentif, C. and Srinivas, S. and Briscoe, J. and Simons, B. D. and Hadjantonakis, A.-K. and Göttgens, B. and Reik, W. and Nichols, J. and Cai, L. and Marioni, J. C. (2021) Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature Biotechnology . ISSN 1087-0156. doi:10.1038/s41587-021-01006-2. (In Press)

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[img] PDF (Supplementary Figs. 1–15 and legend for Supplementary Tables 1–9) - Supplemental Material
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[img] PDF (Reporting Summary) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 1 seqFISH probe library design) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 2 Validation of RNA quality and cell segmentation) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 3 Optimizing cell type annotation) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 4 Unsupervised clustering of seqFISH data) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 5 Cell annotation and constructing the cell-contact map) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 6 Characterization of mixed mesenchymal mesoderm cluster) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 7 Imputation strategy) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 8 Statistical interrogation of the Midbrain-Hindbrain Region) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 9 Surrounding mesoderm of the developing gut tube) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 10 Comparison between dorsal and ventral side of developing gut tube) - Supplemental Material
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Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8–12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain–hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal–ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.

Item Type:Article
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URLURL TypeDescription ReadCube access Paper ItemData ItemCode
Lohoff, T.0000-0001-9333-842X
Ghazanfar, S.0000-0001-7861-6997
Missarova, A.0000-0001-9472-2095
Koulena, N.0000-0002-9419-5712
Pierson, N.0000-0002-2451-0633
Griffiths, J. A.0000-0002-2010-2296
Bardot, E. S.0000-0002-0872-4957
Eng, C.-H. L.0000-0002-2521-9696
Tyser, R. C. V.0000-0001-7884-1756
Argelaguet, R.0000-0003-3199-3722
Guibentif, C.0000-0001-8457-456X
Srinivas, S.0000-0001-5726-7791
Briscoe, J.0000-0002-1020-5240
Simons, B. D.0000-0002-3875-7071
Göttgens, B.0000-0001-6302-5705
Reik, W.0000-0003-0216-9881
Cai, L.0000-0002-7154-5361
Alternate Title:Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis
Additional Information:© The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit Received 03 February 2021; Accepted 07 July 2021; Published 06 September 2021. We thank our colleagues in the Wellcome Trust Mouse Gastrulation Consortium as well as colleagues in the University of Cambridge Stem Cell Institute, Cancer Research UK Cambridge Institute, Babraham Institute, Gurdon Institute, California Institute of Technology, Sloan Kettering and the Francis Crick Institute for their support and intellectual engagement. We thank J. Thomassie, E. Buitrago-Delgado, J. Yun, M. Lawson, C. Cronin, C. Karp and other members of the Cai lab for experimental support and constructive input. We thank S. Nowotschin and E. Wershof for discussions concerning the gut tube analysis. We thank V. Juvin for providing scientific illustration. We thank D. Keitley, M. Morgan and other members of the Marioni lab for discussions concerning the analysis. We thank members of the Nichols and Reik lab for their discussions concerning the project. The following sources of funding are gratefully acknowledged. This work was supported by the Wellcome Trust (award 105031/D/14/Z to W.R., J.N., J.C.M., B.G., S.S. and B.D.S.). T.L. was was funded by the Wellcome Trust 4-Year PhD Programme in Stem Cell Biology and Medicine and the University of Cambridge, UK (203813/Z/16/A and 203813/Z/16/Z) and by the Boehringer Ingelheim Fonds travel grant. S.G. was supported by a Royal Society Newton International Fellowship (NIF\R1\181950). A.M. was supported by an NIH award (1OT2OD026673-01, Comprehensive Collaborative, Infrastructure, Mapping and Tools for the HubMAP HIVE (Mapping Component) to J.C.M.). R.A. was funded by the EMBL PhD programme. R.C.V.T. is funded by a British Heart Foundation Immediate Fellowship (FS/18/24/33424). C.G. was supported by funding from the Swedish Research Council (2017-06278). J.B. is supported by the Francis Crick Institute, which receives core funding from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust (all under FC001051). B.D.S. is supported by the Royal Society (EP Abraham Research Professorship, RP\R1\180165) and the Wellcome Trust (219478/Z/19/Z). A.-K.H. was supported by National Institutes of Health (NIH) grants (award numbers R01- DK127821 and P30-CA008748). W.R. is supported by funding from BBSRC ISPG (BBS/E/B/000C0421). B.G. and J.N. are supported by core funding by the MRC and Wellcome Trust to the Wellcome–MRC Cambridge Stem Cell Institute. L.C. was supported by the Paul G. Allen Frontiers Foundation Discovery Center for Cell Lineage Tracing (grant UWSC10142). J.C.M. acknowledges core funding from EMBL and core support from Cancer Research UK (C9545/A29580). The funding sources mentioned above had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the manuscript and in the decision to submit the manuscript for publication. This research was funded in whole or in part by the Wellcome Trust. For the purpose of open access, the author has applied a CC BY public copyright licence to any author accepted manuscript version arising from this submission. Data availability: The spatial transcriptomic map can be explored interactively at, and raw image data are available on request. Processed gene expression data with segmentation information and associated metadata are also available to download and explore online at Processed gene expression data are also available within the R/Bioconductor data package MouseGastrulationData (version 3.13, Code availability: Scripts for downstream analysis are available at These authors contributed equally: T. Lohoff, S. Ghazanfar. Author Contributions: T.L., J.A.G. and C.G. performed the probe library gene selection, with input from W.R., J.N., B.G. and J.C.M. T.L., E.S.B. and J.N. performed embryo collection. T.L., C.-H.L.E. and N.K. performed the seqFISH method and segmentation optimization for mouse embryonic tissue sections. T.L. and N.K. generated the spatial dataset, with supervision from L.C. N.P. performed image processing, including registration, cell segmentation and mRNA spot decoding, with input from L.C. T.L. and A.M. performed optical threshold selection for non-barcoded smFISH images. S.G. performed preprocessing, low-level analyses, batch correction, clustering, integration with other datasets and global visualization and designed the associated website, with input from A.M. and R.A. A.M. performed the imputation analysis. S.G. and A.M. performed analysis surrounding MHB formation. E.S.B. performed HCR imaging experiments, with supervision from A.-K.H. R.C.V.T., C.G., S.S., J.B., B.D.S., A.-K.H., B.G., W.R. and J.N. provided discussion and interpretation of the data and analysis. B.G., W.R., J.N., L.C. and J.C.M. supervised the study. T.L., S.G. and A.M. generated figures. T.L., S.G., A.M. and J.C.M. wrote the manuscript. L.C. and J.C.M. oversaw the entirety of the project. A.M., N.K. and N.P. contributed equally to this project. All authors read and approved the final manuscript. Competing interests: W.R. is a consultant and shareholder of Cambridge Epigenetix. L.C. is the cofounder of Spatial Genomics Inc. and holds patents on seqFISH. The remaining authors declare no competing interests. Peer review information: Nature Biotechnology thanks Maya Kumar, Andreas Moor and Junyue Cao for their contribution to the peer review of this work.
Funding AgencyGrant Number
Wellcome Trust105031/D/14/Z
Wellcome Trust203813/Z/16/A
Wellcome Trust203813/Z/16/Z
Boehringer Ingelheim FondsUNSPECIFIED
Royal SocietyNIF\R1\181950
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
British Heart FoundationFS/18/24/33424
Swedish Research Council2017-06278
Francis Crick InstituteUNSPECIFIED
Medical Research Council (UK)UNSPECIFIED
Wellcome TrustFC001051
Royal SocietyRP\R1\180165
Wellcome Trust219478/Z/19/Z
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/B/000C0421
Paul G. Allen Frontiers GroupUWSC10142
Cancer Research UKC9545/A29580
Subject Keywords:Computational biology and bioinformatics; Embryogenesis
Record Number:CaltechAUTHORS:20201123-133350121
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Official Citation:Lohoff, T., Ghazanfar, S., Missarova, A. et al. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat Biotechnol (2021).
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106790
Deposited By: Tony Diaz
Deposited On:23 Nov 2020 22:16
Last Modified:08 Sep 2021 17:39

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