b, Bar plots of PCC, SSIM, RMSE, and JS of each integration method in predicting the spatial distribution of transcripts of dataset 42. This challenge could be addressed by using cell-type deconvolution approaches or seamless integration with high-resolution tissue images, that is, multicolour immunofluorescence images, to identify the cells in each pixel. Bioinformatics 26, 139140 (2010). Wang, S. et al. 1c, highlighting cells from each sampled time point and therefore illustrating the transcriptional progression along developmental time. 23, 309 (2022). Bioinformatics 31, 166169 (2015). k, Heat map of the gene scores of selected pixels containing a single nucleus. 8 Integrative analysis of spatial-ATAC-seq and scRNA-seq for P21 mouse brain. King, H. W. et al. Nature 521, 316321 (2015). wrote the manuscript with inputs from all authors. For better visualization, we scaled the size of the pixels. Aguilera-Castrejon, A., Oldak, B., Shani, T. et al. 8). Bar charts show the fraction of atlas cells in the myeloid cell cluster mapped to the clusters defined in figure 8 of the previous study54. c, Heatmap of motif hypergeometric enrichment-adjusted P values within the marker peaks of each cluster. These open chromatin regions play important regulatory roles in distinguishing the cell types from complex organisms7. Aligning to the reference genome, the DARs were annotated to promoter, intron, exon, 3 UTR, etc. IEEE Trans. and C.G. 77, 3043 (2017). Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. To systematically investigate the cellular complexity of developing embryonic skin and gain the comprehensive insights into the molecular identity of hair follicle progenitors and niche cells, the nuclei from single-cell suspensions of E13.5, E16.5 and P0 mice dorsal skin were obtained using 10x Genomics ChromiumTM Controller &Accessory Kit. f, Percentages of normal embryos in cultures started at E5.5. Cell 169, 258272 (2017). Hierarchical patterning modes orchestrate hair follicle morphogenesis. These master regulators further validated the unique identity of each cluster. Soft lithography was used for the fabrication of polydimethylsiloxane (PDMS) microfluidic devices. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. ; WK9100000001 to J.L). eCollection 2022. Progenitor cell migrated and then formed the physically identifiable Pc51, placode cells as the earliest progenitors of all epithelial hair follicle cells including adult stem cells (SCs) were in the bulge52. Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci. Genet. Benchmarking spatial and single-cell transcriptomics integration methods. Fig. Right, number of cells captured in this study compared with the estimated number of cells in the embryo from the left panel. Tbx18 targets dermal condensates for labeling, isolation, and gene ablation during embryonic hair follicle formation. & Satija, R. Single-cell chromatin state analysis with Signac. Nat. Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis. m, tdT+ embryos explanted at E7.5 and subjected to in toto live imaging of neural tube closure at E9.0. Performance and QC-related. Images represent a minimum of three biological replicates. BMB Rep. 2022 Mar;55(3):113-124. doi: 10.5483/BMBRep.2022.55.3.014. y axis: ratio of the standard deviation of cell-type frequency to the mean cell-type frequency at different degrees of downsampling. Genet. Cell 17, 365376 (2009). Cell-type-specific marker peaks were identified using the getMarkerFeatures (bias=c(TSSEnrichment, log10(nFrags), testMethod=wilcoxon) and getMarkers (cutOff = FDR<=0.05 & Log2FC>=0.1) functions. Shivdasani, R. A., Mayer, E. L. & Orkin, S. H. Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL. Preprint at https://www.bioRxiv.org/content/early/2018/04/04/234872 (2018). b, Box plots summarizing the density per cell type. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. The tissue was then fixed with formaldehyde (0.2% for 5min) and quenched with glycine (1.25M for 5min) at room temperature. & Dwork, A. J. bg, Gene expression levels of Ttr (b), Mixl1 (c), Nkx2-5 (d), Pyy (e), Nepn (f), and Cdx2 (g), overlaid on the Fig. J. Immunol. Before Nature 563, 7278 (2018). Extended Data Fig. Article 19, 15 (2018). Download : Download high-res image (3MB) Download : Download full-size image; Figure 3. Meijer, D. H. et al. Data are presented as mean values 95% confidence intervals; n=948 predicted genes. ac, Maximum intensity projections of embryos developed ex utero, fixed, and immunostained for eleven specific markers at the indicated time points. A.A.-C. designed and conducted most of the wet lab, embryology, sequencing and imaging experiments, established the ex utero culture protocol and co-wrote the manuscript. 3), coloured by Tal1 expression levels. Brennecke, P. et al. Commun. 7 Spatial chromatin accessibility mapping of E11 mouse embryo and spatiotemporal analysis (20 m pixel size). Mourragui, S., Loog, M., van de Wiel, M. A., Reinders, M. J. T. & Wessels, L. F. A. Metadata for all atlas cells that passed QC. Science 348, aaa6090 (2015). ICML Workshop on Computational Biology (2019). Nodes in f show the frequency of cells from each time point, excluding two samples of mixed time-point embryos. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Dataset 22 (human breast cancer): 10X Visium, CID4290 in https://zenodo.org/record/4739739#.YY6N_pMzaWC; 10X Chromium, CID3586 in GSE176078 in the GEO database. Nat. Schiebinger, G. et al. Robust decomposition of cell type mixtures in spatial transcriptomics. A coordinated progression of progenitor cell states initiates urinary tract development. Nature 373, 432434 (1995). Anders, S., Pyl, P. T. & Huber, W. HTSeqa Python framework to work with high-throughput sequencing data. Resulting DEhindgut 2 trajectory includes clusters 14 and 69. Nat Biotechnol. New, D. A. T. Development of explanted rat embryos in circulating medium. R.S. Ueda, Y. et al. 15, 41234129 (1996). In the meantime, to ensure continued support, we are displaying the site without styles Formation of proximal and anterior limb skeleton requires early function of Irx3 and Irx5 and is negatively regulated by Shh signaling. 2022 Dec 12;12(12):1860. doi: 10.3390/biom12121860. b, Microfluidiccrossflow scheme. Biotechnol. Genome Biol. B.P.-S. and C.G. 10e), consistent with the previous finding that LMO2 is specifically upregulated in the GC50. First, DNA barcode A was annealed with ligation linker 1: 10l of each DNA barcode A (100M), 10l of ligation linker (100M) and 20l of 2 annealing buffer (20mM Tris, pH7.58.0, 100mM NaCl, 2mM EDTA) were added together and mixed well. Nature 566 , 490495 (2019). 2c,h and Supplementary Table 1). Nat. Dataset 43 (mouse hippocampus): ST, wild-type replicate 1 in https://data.mendeley.com/datasets/6s959w2zyr/1; 10X Chromium, GSE116470 in the GEO database. New, D. A. T. Whole-embryo culture and the study of mammalian embryos during organogenesis. 4a,b and5a,b). is CEO of Arad Technologies Ltd. All other authors declare no competing interests. Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves. are funded by the Wellcome 4-Year PhD Programme in Stem Cell Biology and Medicine and the University of Cambridge; D.L.L.H. -, Meehan TF et al. PubMed Central Extended Data Fig. J.B., D.S. Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas. This file contains the full legends for Supplementary Tables 1-6. https://doi.org/10.1038/s41592-022-01480-9. 4 Spatial chromatin accessibility mapping of E11 mouse embryo and spatiotemporal analysis (50 m pixel size). 2003 Aug;273(2):677-80. doi: 10.1002/ar.a.10089. We provide a benchmark pipeline to help researchers select optimal integration methods to process their datasets. We dedicate this paper to the memories of R. Massarwa and H. Garty. As cell type heterogeneity was readily apparent within many of the 38 clusters shown in Fig. Scale bars, 0.25mm. J. CD32, a surface receptor that is involved in phagocytosis and clearing of immune complexes46, and CD55, a complement decay-accelerating factor, were both active in the same region such that the cells that are not supposed to be cleared can be protected against phagocytosis by blocking the formation of the membrane attack complex47. Sci. R.F. Anat Rec A Discov Mol Cell Evol Biol. CAS & He, Q.-Y. 12, 1089 (2021). Maximum intensity projections of embryos developed in utero and ex utero, fixed and immunostained for SOX2, OTX2, TUJ1, PAX6, SOX9, Brachyury, CDX2 and MHC-II (myosin heavy chain-II) at the indicated stages. Nat. A similar decrease in chromatin accessibility was observed in excitatory neurons for a specific intronic enhancer of Nova2, which encodes an RNA-binding protein that is expressed in neurons23. Hu, Y. et al. Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level. 9). n, total number of cultured embryos; x, number of experiments. PUBMED: 34711971 PMC: PMC8566243 Dataset 19 (mouse hindlimb muscle): 10X Visium, Vis9A in GSE161318 in the GEO database; 10X Chromium, D7_Ev3 in GSE159500 in the GEO database. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 583, 744751 (2020). Gmez-Lpez, S. et al. Dataset 9 (mouse VISP): MERFISH, https://github.com/spacetx-spacejam/data/; Smart-seq, mouse primary visual cortex (VISp) in https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-v1-and-alm-smart-seq. 111, 16 (1998). Science 360, 981987 (2018). To further demonstrate the ability to profile spatial chromatin accessibility in different species and tissue types, we applied spatial-ATAC-seq to human tonsil tissue. Scale bars, 500 m. 2a); the 8 populations were fibroblasts, keratinocytes, blood vessels, lymphocytes, macrophages, muscle, schwann and melanocytes (Fig. 19, 423 (2008). 2018 Mar 14;19(1):31. doi: 10.1186/s13059-018-1416-2. Rev. Erratum: Vitamin D sufficiency enhances differentiation of patient-derived prostate epithelial organoids. 2022 Dec 13;23(1):256. doi: 10.1186/s13059-022-02824-6. Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Gttgens B, Reik W, Nichols J, Cai L, Marioni JC. b, c, Top and front views of the gas controller module. WebSingle-Cell Transcriptomic Atlas of Primate Ovarian Aging. Invest Dermatol. c, Integration of scATAC-seq31 from human hippocampus and spatial-ATAC-seq. Nat. A trajectory backbone was first created in the form of an ordered vector of cell group labels. Disclaimer, National Library of Medicine Identification of LMO2 transcriptome and interactome in diffuse large B-cell lymphoma. Eng, C. L. et al. Nature. Rev. 3d). 52, 11581168 (2020). Lopez, R. et al. d, Measurements of embryonic length at the indicated time points. Single-cell chromatin accessibility reveals principles of regulatory variation. & Guo, C. Lang R & R, A. Dermal -catenin activity in response to epidermal Wnt ligands is required for fibroblast proliferation and hair follicle initiation. Thereafter, the epidermis was digested with TE for 15min, while the dermis was digested with 2mg/mL collagenase type II (Sigma, St Louis, MO, USA) for 15min. Finally, the gene activity of some typical cell type-specific marker genes were visualized for clustering and cell type assignment of scATAC-seq data. Scale bar, 25kb. We then identified changes in gene score across this developmental process, and observed high chromatin accessibility in radial glia at Sox2 and Pax6 loci, genes encoding transcription factors that are necessary for progenitor self-renewal identity22. Bedzhov, I. Kalies, K., Blessenohl, M., Nietsch, J. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. c, Efficiency of normal embryonic development evaluated in different mouse genetic backgrounds. Stuart, T. et al. Finally, spatial-ATAC-seq is yet to be further extended to tissue samples from human patients with a disease to realize its full potential in clinical research. Comparative light-sheet 3D reconstruction of ex utero and in utero embryos. To date, the ability to spatially map epigenetic states, such as chromatin accessibility, directly in a tissue section at the genome scale and cellular level is lacking. a, Protocol for differentiation of microglia progenitors from humans ES cells as previously described28. Mouse C57 Embryo Sagittal Frozen Sections (MF-104-11-C57) and Human Tonsil Frozen Sections (HF-707) were purchased from Zyagen. FOIA is funded by the Wellcome Mathematical Genomics and Medicine Programme at the University of Cambridge (109081/Z/15/A). Data are presented as mean values 95% confidence intervals; n=19 independent datasets. Comprehensive integration of single-cell data. PYS, parietal yolk sac; RS, rat serum. ISSN 2052-4463 (online). Single-cell RNA-seq of mouse olfactory bulb reveals cellular heterogeneity and activity-dependent molecular census of adult-born neurons. is funded by the Swedish Research Council (2017-06278, administered by Sahlgrenska Cancer Center, University of Gothenburg). a, Spatial distribution of Cplx1 expression in dataset 4 (seqFISH+; Smart-seq; mouse cortex), predicted from the original data and down-sampled data (down-sampling rate = 0.8). The datasets here provided the single-cell epigenomic profiling of hair follicle cells from the skin at different stages of mouse embryonic development. Lyu, P. et al. We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. High-definition spatial transcriptomics for in situ tissue profiling. Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics. Song, Q. Q. h, Spatial mapping of selected cell types identified by label transfer from scRNA-seq to spatial-ATAC-seq. For barcode B in situ ligation, the second PDMS slab with channels perpendicular to the first PDMS was attached to the dried slide carefully. CAS Protoc. WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition. Huang, Y., Osorno, R., Tsakiridis, A. In E13.5, we found that clusters 0, 1 and 2 mainly expressed fibroblast markers of Twist228 and Col1a129, clusters 3 and 8 expressed keratinocytes markers of Krt1430 and Krt1531, cluster 4 expressed macrophages markers of Cd8632 and Inpp5d33, cluster 5 expressed schwann markers of Sox56 and Sox1034, cluster 6 expressed blood vessels markers of Pecam135 and Kdr36,37, cluster 7 expressed muscle markers of Pax730 and Cdh1538. https://doi.org/10.1038/s41586-019-0933-9. Berkeley Drosophila Transcription Network Project. Federal government websites often end in .gov or .mil. It was found that the percentage of fibroblasts was gradually decreased (E13.5: 63.5%; E16.5: 57.8%; P0: 47.8%) and the percentage of keratinocytes was gradually increased (E13.5: 16.8%; E16.5: 17.5%; P0: 43.6%). B.P.-S., W.J., F.J.C.-N., C.M. & Duboule, D. Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock. Science 360, 981987 (2018). Cell 161, 12021214 (2015). Nature 598, 129136 (2021). Exch. Janosevic, D. et al. CAS g, Pseudotemporal reconstruction from the developmental process from radial glia, postmitotic premature neurons, to excitatory neurons plotted in space. f, Interior of the precision incubator system (by B.T.C. d, e, Picture displaying the localization of the main components in the gas regulation module (d; listed in e). Furthermore, we tested the sensitivity of different Tn5 transposase enzymes (Diagenode (C01070010) versus Lucigen (TNP92110)). volume566,pages 490495 (2019)Cite this article. The functional and molecular divergence of OLIG1 and OLIG2. Dataset 31 (mouse brain): 10X Visium, section1 in GSE153424 in the GEO database; 10X Chromium, brain1_cx in GSE153424 in the GEO database. -, Dickinson ME et al. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
