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Volumn 33, Issue 5, 2015, Pages 495-502

Spatial reconstruction of single-cell gene expression data

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CYTOLOGY; GENES; HISTOLOGY; MAPPING; MOBILE SECURITY; RNA; TISSUE;

EID: 84929151009     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3192     Document Type: Article
Times cited : (3769)

References (50)
  • 1
    • 79953043801 scopus 로고    scopus 로고
    • The developmental transcriptome of Drosophila melanogaster
    • Graveley, B.R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479 (2011).
    • (2011) Nature , vol.471 , pp. 473-479
    • Graveley, B.R.1
  • 2
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • Gerstein, M.B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787 (2010).
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1
  • 3
    • 84876801883 scopus 로고    scopus 로고
    • Genomics: Zebrafish earns its stripes
    • Schier, A.F. Genomics: zebrafish earns its stripes. Nature 496, 443-444 (2013).
    • (2013) Nature , vol.496 , pp. 443-444
    • Schier, A.F.1
  • 4
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1160-1167
    • Islam, S.1
  • 5
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells
    • Ramsköld, D. et al. Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30, 777-782 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 777-782
    • Ramsköld, D.1
  • 6
    • 84893905629 scopus 로고    scopus 로고
    • Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
    • Jaitin, D.A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776-779 (2014).
    • (2014) Science , vol.343 , pp. 776-779
    • Jaitin, D.A.1
  • 7
    • 84922321862 scopus 로고    scopus 로고
    • Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
    • Pollen, A.A. et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat. Biotechnol. 32, 1053-1058 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 1053-1058
    • Pollen, A.A.1
  • 8
    • 84878997106 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    • Shalek, A.K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
    • (2013) Nature , vol.498 , pp. 236-240
    • Shalek, A.K.1
  • 9
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1
  • 10
    • 84900529199 scopus 로고    scopus 로고
    • Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
    • Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371-375 (2014).
    • (2014) Nature , vol.509 , pp. 371-375
    • Treutlein, B.1
  • 11
    • 84866953427 scopus 로고    scopus 로고
    • CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification
    • Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Reports 2, 666-673 (2012).
    • (2012) Cell Reports , vol.2 , pp. 666-673
    • Hashimshony, T.1    Wagner, F.2    Sher, N.3    Yanai, I.4
  • 12
    • 84892179132 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
    • Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193-196 (2014).
    • (2014) Science , vol.343 , pp. 193-196
    • Deng, Q.1    Ramsköld, D.2    Reinius, B.3    Sandberg, R.4
  • 13
    • 84895071445 scopus 로고    scopus 로고
    • Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue
    • Lovatt, D. et al. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat. Methods 11, 190-196 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 190-196
    • Lovatt, D.1
  • 14
    • 84897090228 scopus 로고    scopus 로고
    • Highly multiplexed subcellular RNA sequencing in situ
    • Lee, J.-H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science 343, 1360-1363 (2014).
    • (2014) Science , vol.343 , pp. 1360-1363
    • Lee, J.-H.1
  • 15
    • 0027226233 scopus 로고
    • Commitment of cell fate in the early zebrafish embryo
    • Ho, R. & Kimmel, C. Commitment of cell fate in the early zebrafish embryo. Science 261, 109-111 (1993).
    • (1993) Science , vol.261 , pp. 109-111
    • Ho, R.1    Kimmel, C.2
  • 16
    • 28944448921 scopus 로고    scopus 로고
    • Molecular genetics of axis formation in zebrafish
    • Schier, A.F. & Talbot, W.S. Molecular genetics of axis formation in zebrafish. Annu. Rev. Genet. 39, 561-613 (2005).
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 561-613
    • Schier, A.F.1    Talbot, W.S.2
  • 17
    • 0025270337 scopus 로고
    • Origin and organization of the zebrafish fate map
    • Kimmel, C.B., Warga, R.M. & Schilling, T.F. Origin and organization of the zebrafish fate map. Development 108, 581-594 (1990).
    • (1990) Development , vol.108 , pp. 581-594
    • Kimmel, C.B.1    Warga, R.M.2    Schilling, T.F.3
  • 18
    • 84856973947 scopus 로고    scopus 로고
    • Breaking symmetry: The zebrafish as a model for understanding left-right asymmetry in the developing brain
    • Roussigné, M., Blader, P. & Wilson, S.W. Breaking symmetry: the zebrafish as a model for understanding left-right asymmetry in the developing brain. Dev. Neurobiol. 72, 269-281 (2012).
    • (2012) Dev. Neurobiol. , vol.72 , pp. 269-281
    • Roussigné, M.1    Blader, P.2    Wilson, S.W.3
  • 20
    • 84900346600 scopus 로고    scopus 로고
    • Reconstruction of the mouse otocyst and early neuroblast lineage at single-cell resolution
    • Durruthy-Durruthy, R. et al. Reconstruction of the mouse otocyst and early neuroblast lineage at single-cell resolution. Cell 157, 964-978 (2014).
    • (2014) Cell , vol.157 , pp. 964-978
    • Durruthy-Durruthy, R.1
  • 21
    • 84887109584 scopus 로고    scopus 로고
    • Accounting for technical noise in single-cell RNA-seq experiments
    • Brennecke, P. et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10, 1093-1095 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1093-1095
    • Brennecke, P.1
  • 22
    • 84903574951 scopus 로고    scopus 로고
    • Bayesian approach to single-cell differential expression analysis
    • Kharchenko, P.V., Silberstein, L. & Scadden, D.T. Bayesian approach to single-cell differential expression analysis. Nat. Methods 11, 740-742 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 740-742
    • Kharchenko, P.V.1    Silberstein, L.2    Scadden, D.T.3
  • 24
    • 84876528441 scopus 로고    scopus 로고
    • ZFIN, the Zebrafish Model Organism Database: Increased support for mutants and transgenics
    • Howe, D.G. et al. ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. 41, D854-D860 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D854-D860
    • Howe, D.G.1
  • 25
    • 0035214296 scopus 로고    scopus 로고
    • A gene expression screen in zebrafish embryogenesis
    • Kudoh, T. et al. A gene expression screen in zebrafish embryogenesis. Genome Res. 11, 1979-1987 (2001).
    • (2001) Genome Res , vol.11 , pp. 1979-1987
    • Kudoh, T.1
  • 26
    • 16644391747 scopus 로고    scopus 로고
    • Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening
    • Thisse, B. et al. Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening. Methods Cell Biol. 77, 505-519 (2004).
    • (2004) Methods Cell Biol. , vol.77 , pp. 505-519
    • Thisse, B.1
  • 28
    • 84901831004 scopus 로고    scopus 로고
    • Validation of noise models for single-cell transcriptomics
    • Grün, D., Kester, L. & van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat. Methods 11, 637-640 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 637-640
    • Grün, D.1    Kester, L.2    Van Oudenaarden, A.3
  • 29
    • 84903185013 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
    • Shalek, A.K. et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510, 363-369 (2014).
    • (2014) Nature , vol.510 , pp. 363-369
    • Shalek, A.K.1
  • 31
    • 3042623646 scopus 로고    scopus 로고
    • Skin development in bony fish with particular emphasis on collagen deposition in the dermis of the zebrafish (Danio rerio)
    • Le Guellec, D., Morvan-Dubois, G. & Sire, J.-Y. Skin development in bony fish with particular emphasis on collagen deposition in the dermis of the zebrafish (Danio rerio). Int. J. Dev. Biol. 48, 217-231 (2004).
    • (2004) Int. J. Dev. Biol. , vol.48 , pp. 217-231
    • Le Guellec, D.1    Morvan-Dubois, G.2    Sire, J.-Y.3
  • 32
    • 0035875826 scopus 로고    scopus 로고
    • Casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish
    • Kikuchi, Y. Casanova encodes a novel Sox-related protein necessary and sufficient for early endoderm formation in zebrafish. Genes Dev. 15, 1493-1505 (2001).
    • (2001) Genes Dev. , vol.15 , pp. 1493-1505
    • Kikuchi, Y.1
  • 33
    • 0030928578 scopus 로고    scopus 로고
    • Zebrafish vasa homologue RNA is localized to the cleavage planes of 2- and 4-cell-stage embryos and is expressed in the primordial germ cells
    • Yoon, C., Kawakami, K. & Hopkins, N. Zebrafish vasa homologue RNA is localized to the cleavage planes of 2- and 4-cell-stage embryos and is expressed in the primordial germ cells. Development 124, 3157-3165 (1997).
    • (1997) Development , vol.124 , pp. 3157-3165
    • Yoon, C.1    Kawakami, K.2    Hopkins, N.3
  • 34
    • 0027278279 scopus 로고
    • Lithium perturbation and goosecoid expression identify a dorsal specification pathway in the pregastrula zebrafish
    • Stachel, S.E., Grunwald, D.J. & Myers, P.Z. Lithium perturbation and goosecoid expression identify a dorsal specification pathway in the pregastrula zebrafish. Development 117, 1261-1274 (1993).
    • (1993) Development , vol.117 , pp. 1261-1274
    • Stachel, S.E.1    Grunwald, D.J.2    Myers, P.Z.3
  • 35
    • 0345426298 scopus 로고    scopus 로고
    • Three different noggin genes antagonize the activity of bone morphogenetic proteins in the zebrafish embryo
    • Fürthauer, M., Thisse, B. & Thisse, C. Three different noggin genes antagonize the activity of bone morphogenetic proteins in the zebrafish embryo. Dev. Biol. 214, 181-196 (1999).
    • (1999) Dev. Biol. , vol.214 , pp. 181-196
    • Fürthauer, M.1    Thisse, B.2    Thisse, C.3
  • 36
    • 0034710967 scopus 로고    scopus 로고
    • Antagonistic role of vega1 and bozozok/dharma homeobox genes in organizer formation
    • Kawahara, A., Wilm, T., Solnica-Krezel, L. & Dawid, I.B. Antagonistic role of vega1 and bozozok/dharma homeobox genes in organizer formation. Proc. Natl. Acad. Sci. USA 97, 12121-12126 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12121-12126
    • Kawahara, A.1    Wilm, T.2    Solnica-Krezel, L.3    Dawid, I.B.4
  • 37
    • 0031959593 scopus 로고    scopus 로고
    • Expression of two zebrafish homologues of the murine Six3 gene demarcates the initial eye primordia
    • Seo, H.-C., Drivenes, Ø., Ellingsen, S. & Fjose, A. Expression of two zebrafish homologues of the murine Six3 gene demarcates the initial eye primordia. Mech. Dev. 73, 45-57 (1998).
    • (1998) Mech. Dev. , vol.73 , pp. 45-57
    • Seo, H.-C.1    Drivenes Ø.2    Ellingsen, S.3    Fjose, A.4
  • 38
    • 84880835682 scopus 로고    scopus 로고
    • Full transcriptome analysis of early dorsoventral patterning in zebrafish
    • Fodor, E. et al. Full transcriptome analysis of early dorsoventral patterning in zebrafish. PLoS ONE 8, e70053 (2013).
    • (2013) PLoS ONE , vol.8
    • Fodor, E.1
  • 39
    • 84891749518 scopus 로고    scopus 로고
    • Toddler: An embryonic signal that promotes cell movement via Apelin receptors
    • Pauli, A. et al. Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343, 1248636 (2014).
    • (2014) Science , vol.343 , pp. 1248636
    • Pauli, A.1
  • 40
    • 84929166604 scopus 로고    scopus 로고
    • High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
    • 13 April
    • Achim, K. et al. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat. Biotechnol. 33, doi:10.1038/nbt.3209 (13 April 2015).
    • (2015) Nat. Biotechnol. , vol.33
    • Achim, K.1
  • 41
    • 84881505548 scopus 로고    scopus 로고
    • Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression
    • Combs, P.A. & Eisen, M.B. Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. PLoS ONE 8, e71820 (2013).
    • (2013) PLoS ONE , vol.8
    • Combs, P.A.1    Eisen, M.B.2
  • 42
    • 84908338722 scopus 로고    scopus 로고
    • Genome-wide RNA tomography in the zebrafish embryo
    • Junker, J.P. et al. Genome-wide RNA tomography in the zebrafish embryo. Cell 159, 662-675 (2014).
    • (2014) Cell , vol.159 , pp. 662-675
    • Junker, J.P.1
  • 43
    • 84857836107 scopus 로고    scopus 로고
    • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • Pauli, A. et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22, 577-591 (2012).
    • (2012) Genome Res. , vol.22 , pp. 577-591
    • Pauli, A.1
  • 44
    • 34047255894 scopus 로고    scopus 로고
    • Nodal signaling activates differentiation genes during zebrafish gastrulation
    • Bennett, J.T. et al. Nodal signaling activates differentiation genes during zebrafish gastrulation. Dev. Biol. 304, 525-540 (2007).
    • (2007) Dev. Biol. , vol.304 , pp. 525-540
    • Bennett, J.T.1
  • 45
    • 0027453569 scopus 로고
    • Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos
    • Thisse, C., Thisse, B., Schilling, T.F. & Postlethwait, J.H. Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos. Development 119, 1203-1215 (1993).
    • (1993) Development , vol.119 , pp. 1203-1215
    • Thisse, C.1    Thisse, B.2    Schilling, T.F.3    Postlethwait, J.H.4
  • 46
    • 25144514023 scopus 로고    scopus 로고
    • Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification
    • Clay, H. & Ramakrishnan, L. Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification. Zebrafish 2, 105-111 (2005).
    • (2005) Zebrafish , vol.2 , pp. 105-111
    • Clay, H.1    Ramakrishnan, L.2
  • 47
    • 84928983540 scopus 로고    scopus 로고
    • Statistical significance of variables driving systematic variation in high-dimensional data
    • Chung, N.C. & Storey, J.D. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics 31, 545-554 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 545-554
    • Chung, N.C.1    Storey, J.D.2
  • 48
    • 70450203033 scopus 로고    scopus 로고
    • Mixtools: An R package for analyzing finite mixture models
    • Benaglia, T., Chauveau, D., Hunter, D. & Young, D. Mixtools: an R package for analyzing finite mixture models. J. Stat. Softw. 32, 1-29 (2009).
    • (2009) J. Stat. Softw. , vol.32 , pp. 1-29
    • Benaglia, T.1    Chauveau, D.2    Hunter, D.3    Young, D.4
  • 49
    • 84874321000 scopus 로고    scopus 로고
    • Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    • McDavid, A. et al. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics 29, 461-467 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 461-467
    • McDavid, A.1
  • 50
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1


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