메뉴 건너뛰기




Volumn 556, Issue 7699, 2018, Pages 108-112

Whole-organism clone tracing using single-cell sequencing

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; TRANSCRIPTOME;

EID: 85045151597     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature25969     Document Type: Article
Times cited : (302)

References (57)
  • 1
    • 0017618537 scopus 로고
    • Post-embryonic cell lineages of the nematode, Caenorhabditis elegans
    • Sulston, J. E. & Horvitz, H. R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110-156 (1977).
    • (1977) Dev. Biol. , vol.56 , pp. 110-156
    • Sulston, J.E.1    Horvitz, H.R.2
  • 2
    • 56449123775 scopus 로고    scopus 로고
    • Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy
    • Keller, P. J., Schmidt, A. D., Wittbrodt, J. & Stelzer, E. H. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065-1069 (2008).
    • (2008) Science , vol.322 , pp. 1065-1069
    • Keller, P.J.1    Schmidt, A.D.2    Wittbrodt, J.3    Stelzer, E.H.4
  • 3
    • 35948992641 scopus 로고    scopus 로고
    • Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system
    • Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56-62 (2007).
    • (2007) Nature , vol.450 , pp. 56-62
    • Livet, J.1
  • 4
    • 84907737648 scopus 로고    scopus 로고
    • Genome sequencing of normal cells reveals developmental lineages and mutational processes
    • Behjati, S. et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 513, 422-425 (2014).
    • (2014) Nature , vol.513 , pp. 422-425
    • Behjati, S.1
  • 5
    • 79960940121 scopus 로고    scopus 로고
    • Colon stem cell and crypt dynamics exposed by cell lineage reconstruction
    • Reizel, Y. et al. Colon stem cell and crypt dynamics exposed by cell lineage reconstruction. PLoS Genet. 7, e1002192 (2011).
    • (2011) PLoS Genet. , vol.7 , pp. e1002192
    • Reizel, Y.1
  • 6
    • 84908125658 scopus 로고    scopus 로고
    • Clonal dynamics of native haematopoiesis
    • Sun, J. et al. Clonal dynamics of native haematopoiesis. Nature 514, 322-327 (2014).
    • (2014) Nature , vol.514 , pp. 322-327
    • Sun, J.1
  • 7
    • 84876297531 scopus 로고    scopus 로고
    • Diverse and heritable lineage imprinting of early haematopoietic progenitors
    • Naik, S. H. et al. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature 496, 229-232 (2013).
    • (2013) Nature , vol.496 , pp. 229-232
    • Naik, S.H.1
  • 8
    • 84974576984 scopus 로고    scopus 로고
    • Whole-organism lineage tracing by combinatorial and cumulative genome editing
    • McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016).
    • (2016) Science , vol.353 , pp. aaf7907
    • McKenna, A.1
  • 9
    • 84992747353 scopus 로고    scopus 로고
    • CRISPR-barcoding for intratumor genetic heterogeneity modeling and functional analysis of oncogenic driver mutations
    • Guernet, A. et al. CRISPR-barcoding for intratumor genetic heterogeneity modeling and functional analysis of oncogenic driver mutations. Mol. Cell 63, 526-538 (2016).
    • (2016) Mol. Cell , vol.63 , pp. 526-538
    • Guernet, A.1
  • 10
    • 85019143041 scopus 로고    scopus 로고
    • Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding
    • Schmidt, S. T., Zimmerman, S. M., Wang, J., Kim, S. K. & Quake, S. R. Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. ACS Synth. Biol. 6, 936-942 (2017).
    • (2017) ACS Synth. Biol. , vol.6 , pp. 936-942
    • Schmidt, S.T.1    Zimmerman, S.M.2    Wang, J.3    Kim, S.K.4    Quake, S.R.5
  • 11
    • 85002263454 scopus 로고    scopus 로고
    • Rapidly evolving homing CRISPR barcodes
    • Kalhor, R., Mali, P. & Church, G. M. Rapidly evolving homing CRISPR barcodes. Nat. Methods 14, 195-200 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 195-200
    • Kalhor, R.1    Mali, P.2    Church, G.M.3
  • 12
    • 85016160400 scopus 로고    scopus 로고
    • Synthetic recording and in situ readout of lineage information in single cells
    • Frieda, K. L. et al. Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107-111 (2017).
    • (2017) Nature , vol.541 , pp. 107-111
    • Frieda, K.L.1
  • 14
    • 85028346710 scopus 로고    scopus 로고
    • Polylox barcoding reveals haematopoietic stem cell fates realized in vivo
    • Pei, W. et al. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature 548, 456-460 (2017).
    • (2017) Nature , vol.548 , pp. 456-460
    • Pei, W.1
  • 15
    • 85017360311 scopus 로고    scopus 로고
    • Scaling single-cell genomics from phenomenology to mechanism
    • Tanay, A. & Regev, A. Scaling single-cell genomics from phenomenology to mechanism. Nature 541, 331-338 (2017).
    • (2017) Nature , vol.541 , pp. 331-338
    • Tanay, A.1    Regev, A.2
  • 16
    • 84882788354 scopus 로고    scopus 로고
    • Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system
    • Jao, L. E., Wente, S. R. & Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 13904-13909 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 13904-13909
    • Jao, L.E.1    Wente, S.R.2    Chen, W.3
  • 17
    • 0035709955 scopus 로고    scopus 로고
    • A zebrafish histone variant H2A. F/Z and a transgenic H2A.F/Z:GFP fusion protein for in vivo studies of embryonic development
    • Pauls, S., Geldmacher-Voss, B. & Campos-Ortega, J. A. A zebrafish histone variant H2A.F/Z and a transgenic H2A.F/Z:GFP fusion protein for in vivo studies of embryonic development. Dev. Genes Evol. 211, 603-610 (2001).
    • (2001) Dev. Genes Evol. , vol.211 , pp. 603-610
    • Pauls, S.1    Geldmacher-Voss, B.2    Campos-Ortega, J.A.3
  • 18
    • 84994589771 scopus 로고    scopus 로고
    • A single-cell transcriptome atlas of the human pancreas
    • Muraro, M. J. et al. A single-cell transcriptome atlas of the human pancreas. Cell Syst. 3, 385-394.e3 (2016).
    • (2016) Cell Syst. , vol.3 , pp. 385e3-394e3
    • Muraro, M.J.1
  • 19
    • 84996605620 scopus 로고    scopus 로고
    • Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development
    • Henninger, J. et al. Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development. Nat. Cell Biol. 19, 17-27 (2017).
    • (2017) Nat. Cell Biol. , vol.19 , pp. 17-27
    • Henninger, J.1
  • 20
    • 84941201582 scopus 로고    scopus 로고
    • Single-cell messenger RNA sequencing reveals rare intestinal cell types
    • Grün, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251-255 (2015).
    • (2015) Nature , vol.525 , pp. 251-255
    • Grün, D.1
  • 21
    • 79959659104 scopus 로고    scopus 로고
    • Zebrafish as a model for normal and malignant hematopoiesis
    • Jing, L. & Zon, L. I. Zebrafish as a model for normal and malignant hematopoiesis. Dis. Model. Mech. 4, 433-438 (2011).
    • (2011) Dis. Model. Mech. , vol.4 , pp. 433-438
    • Jing, L.1    Zon, L.I.2
  • 22
    • 84942523027 scopus 로고    scopus 로고
    • Temporal-spatial resolution fate mapping reveals distinct origins for embryonic and adult microglia in zebrafish
    • Xu, J. et al. Temporal-spatial resolution fate mapping reveals distinct origins for embryonic and adult microglia in zebrafish. Dev. Cell 34, 632-641 (2015).
    • (2015) Dev. Cell , vol.34 , pp. 632-641
    • Xu, J.1
  • 23
    • 84874007223 scopus 로고    scopus 로고
    • Neurogenesis in zebrafish - from embryo to adult
    • Schmidt, R., Strähle, U. & Scholpp, S. Neurogenesis in zebrafish - from embryo to adult. Neural Dev. 8, 3 (2013).
    • (2013) Neural Dev. , vol.8 , pp. 3
    • Schmidt, R.1    Strähle, U.2    Scholpp, S.3
  • 24
    • 84879673968 scopus 로고    scopus 로고
    • An exclusively mesodermal origin of fin mesenchyme demonstrates that zebrafish trunk neural crest does not generate ectomesenchyme
    • Lee, R. T., Knapik, E. W., Thiery, J. P. & Carney, T. J. An exclusively mesodermal origin of fin mesenchyme demonstrates that zebrafish trunk neural crest does not generate ectomesenchyme. Development 140, 2923-2932 (2013).
    • (2013) Development , vol.140 , pp. 2923-2932
    • Lee, R.T.1    Knapik, E.W.2    Thiery, J.P.3    Carney, T.J.4
  • 25
    • 79955918159 scopus 로고    scopus 로고
    • Fate restriction in the growing and regenerating zebrafish fin
    • Tu, S. & Johnson, S. L. Fate restriction in the growing and regenerating zebrafish fin. Dev. Cell 20, 725-732 (2011).
    • (2011) Dev. Cell , vol.20 , pp. 725-732
    • Tu, S.1    Johnson, S.L.2
  • 26
    • 79955926225 scopus 로고    scopus 로고
    • Bone regenerates via dedifferentiation of osteoblasts in the zebrafish fin
    • Knopf, F. et al. Bone regenerates via dedifferentiation of osteoblasts in the zebrafish fin. Dev. Cell 20, 713-724 (2011).
    • (2011) Dev. Cell , vol.20 , pp. 713-724
    • Knopf, F.1
  • 27
    • 84859845794 scopus 로고    scopus 로고
    • Regeneration of amputated zebrafish fin rays from de novo osteoblasts
    • Singh, S. P., Holdway, J. E. & Poss, K. D. Regeneration of amputated zebrafish fin rays from de novo osteoblasts. Dev. Cell 22, 879-886 (2012).
    • (2012) Dev. Cell , vol.22 , pp. 879-886
    • Singh, S.P.1    Holdway, J.E.2    Poss, K.D.3
  • 28
    • 84997199395 scopus 로고    scopus 로고
    • Live monitoring of blastemal cell contributions during appendage regeneration
    • Tornini, V. A. et al. Live monitoring of blastemal cell contributions during appendage regeneration. Curr. Biol. 26, 2981-2991 (2016).
    • (2016) Curr. Biol. , vol.26 , pp. 2981-2991
    • Tornini, V.A.1
  • 29
    • 85027552898 scopus 로고    scopus 로고
    • Live fate-mapping of joint-associated fibroblasts visualizes expansion of cell contributions during zebrafish fin regeneration
    • Tornini, V. A., Thompson, J. D., Allen, R. L. & Poss, K. D. Live fate-mapping of joint-associated fibroblasts visualizes expansion of cell contributions during zebrafish fin regeneration. Development 144, 2889-2895 (2017).
    • (2017) Development , vol.144 , pp. 2889-2895
    • Tornini, V.A.1    Thompson, J.D.2    Allen, R.L.3    Poss, K.D.4
  • 30
    • 84867740805 scopus 로고    scopus 로고
    • Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages
    • Gautier, E. L. et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat. Immunol. 13, 1118-1128 (2012).
    • (2012) Nat. Immunol. , vol.13 , pp. 1118-1128
    • Gautier, E.L.1
  • 31
    • 85045131214 scopus 로고    scopus 로고
    • Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
    • Raj, B. et al. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat. Biotechnol. http://doi.org/10.1038/nbt.4103 (2018).
    • (2018) Nat. Biotechnol
    • Raj, B.1
  • 32
    • 85045136951 scopus 로고    scopus 로고
    • Simultaneous lineage tracing and cell-type identification using CRISPR/Cas9-induced genetic scars
    • Spanjaard, B. et al. Simultaneous lineage tracing and cell-type identification using CRISPR/Cas9-induced genetic scars. Nat. Biotechnol. https://doi. org/10.1038/nbt/4124 (2018).
    • (2018) Nat. Biotechnol
    • Spanjaard, B.1
  • 34
    • 79955602650 scopus 로고    scopus 로고
    • Cellular dissection of zebrafish hematopoiesis
    • Stachura, D. L. & Traver, D. Cellular dissection of zebrafish hematopoiesis. Methods Cell Biol. 101, 75-110 (2011).
    • (2011) Methods Cell Biol. , vol.101 , pp. 75-110
    • Stachura, D.L.1    Traver, D.2
  • 36
    • 0034659909 scopus 로고    scopus 로고
    • Roles for Fgf signaling during zebrafish fin regeneration
    • Poss, K. D. et al. Roles for Fgf signaling during zebrafish fin regeneration. Dev. Biol. 222, 347-358 (2000).
    • (2000) Dev. Biol. , vol.222 , pp. 347-358
    • Poss, K.D.1
  • 37
    • 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
  • 38
    • 75649102550 scopus 로고    scopus 로고
    • Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells
    • Kobayashi, I. et al. Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells. Blood 115, e1-e9 (2010).
    • (2010) Blood , vol.115 , pp. e1-e9
    • Kobayashi, I.1
  • 39
    • 84971518932 scopus 로고    scopus 로고
    • Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish
    • Moore, F. E. et al. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish. J. Exp. Med. 213, 979-992 (2016).
    • (2016) J. Exp. Med. , vol.213 , pp. 979-992
    • Moore, F.E.1
  • 40
    • 84958103478 scopus 로고    scopus 로고
    • Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells
    • Macaulay, I. C. et al. Single-cell RNA-sequencing reveals a continuous spectrum of differentiation in hematopoietic cells. Cell Reports 14, 966-977 (2016).
    • (2016) Cell Reports , vol.14 , pp. 966-977
    • Macaulay, I.C.1
  • 41
    • 85016468947 scopus 로고    scopus 로고
    • Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types
    • Carmona, S. J. et al. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res. 27, 451-461 (2017).
    • (2017) Genome Res. , vol.27 , pp. 451-461
    • Carmona, S.J.1
  • 42
    • 38149129457 scopus 로고    scopus 로고
    • A transcriptome database for astrocytes, neurons, and oligodendrocytes: A new resource for understanding brain development and function
    • Cahoy, J. D. et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264-278 (2008).
    • (2008) J. Neurosci. , vol.28 , pp. 264-278
    • Cahoy, J.D.1
  • 43
    • 54549092620 scopus 로고    scopus 로고
    • The developmental sequence of gene expression within the rod photoreceptor lineage in embryonic zebrafish
    • Nelson, S. M., Frey, R. A., Wardwell, S. L. & Stenkamp, D. L. The developmental sequence of gene expression within the rod photoreceptor lineage in embryonic zebrafish. Dev. Dyn. 237, 2903-2917 (2008).
    • (2008) Dev. Dyn. , vol.237 , pp. 2903-2917
    • Nelson, S.M.1    Frey, R.A.2    Wardwell, S.L.3    Stenkamp, D.L.4
  • 44
    • 84866504650 scopus 로고    scopus 로고
    • Differential recruitment of brain networks following route and cartographic map learning of spatial environments
    • Zhang, H., Copara, M. & Ekstrom, A. D. Differential recruitment of brain networks following route and cartographic map learning of spatial environments. PLoS ONE 7, e44886 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e44886
    • Zhang, H.1    Copara, M.2    Ekstrom, A.D.3
  • 45
    • 84888324248 scopus 로고    scopus 로고
    • The microglial sensome revealed by direct RNA sequencing
    • Hickman, S. E. et al. The microglial sensome revealed by direct RNA sequencing. Nat. Neurosci. 16, 1896-1905 (2013).
    • (2013) Nat. Neurosci. , vol.16 , pp. 1896-1905
    • Hickman, S.E.1
  • 46
    • 84872475557 scopus 로고    scopus 로고
    • Characterization of the calcium binding protein family in zebrafish
    • Di Donato, V., Auer, T. O., Duroure, K. & Del Bene, F. Characterization of the calcium binding protein family in zebrafish. PLoS ONE 8, e53299 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e53299
    • Di Donato, V.1    Auer, T.O.2    Duroure, K.3    Del Bene, F.4
  • 47
    • 84876555679 scopus 로고    scopus 로고
    • Allen Brain Atlas: An integrated spatio-temporal portal for exploring the central nervous system
    • Sunkin, S. M. et al. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Res. 41, D996-D1008 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D996-D1008
    • Sunkin, S.M.1
  • 48
    • 84990876505 scopus 로고    scopus 로고
    • Molecular diversity of midbrain development in mouse, human, and stem cells
    • La Manno, G. et al. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell 167, 566-580 (2016).
    • (2016) Cell , vol.167 , pp. 566-580
    • La Manno, G.1
  • 49
    • 84975165639 scopus 로고    scopus 로고
    • Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system
    • Marques, S. et al. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 352, 1326-1329 (2016).
    • (2016) Science , vol.352 , pp. 1326-1329
    • Marques, S.1
  • 50
    • 85016318044 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals hypothalamic cell diversity
    • Chen, R., Wu, X., Jiang, L. & Zhang, Y. Single-cell RNA-seq reveals hypothalamic cell diversity. Cell Reports 18, 3227-3241 (2017).
    • (2017) Cell Reports , vol.18 , pp. 3227-3241
    • Chen, R.1    Wu, X.2    Jiang, L.3    Zhang, Y.4
  • 51
    • 84991670933 scopus 로고    scopus 로고
    • Identification of a conserved and acute neurodegenerationspecific microglial transcriptome in the zebrafish
    • Oosterhof, N. et al. Identification of a conserved and acute neurodegenerationspecific microglial transcriptome in the zebrafish. Glia 65, 138-149 (2017).
    • (2017) Glia , vol.65 , pp. 138-149
    • Oosterhof, N.1
  • 52
    • 42749092987 scopus 로고    scopus 로고
    • Transcription factors controlling osteoblastogenesis
    • Marie, P. J. Transcription factors controlling osteoblastogenesis. Arch. Biochem. Biophys. 473, 98-105 (2008).
    • (2008) Arch. Biochem. Biophys. , vol.473 , pp. 98-105
    • Marie, P.J.1
  • 53
    • 84921985799 scopus 로고    scopus 로고
    • Spatial and temporal control of transgene expression in zebrafish
    • Akerberg, A. A., Stewart, S. & Stankunas, K. Spatial and temporal control of transgene expression in zebrafish. PLoS ONE 9, e92217 (2014).
    • (2014) PLoS ONE , vol.9 , pp. e92217
    • Akerberg, A.A.1    Stewart, S.2    Stankunas, K.3
  • 54
    • 4544312319 scopus 로고    scopus 로고
    • The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis
    • Smyth, I. et al. The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis. Proc. Natl Acad. Sci. USA 101, 13560-13565 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 13560-13565
    • Smyth, I.1
  • 55
    • 85040094342 scopus 로고
    • On optimal and data-based histograms
    • Scott, D. On optimal and data-based histograms. Biometrika 66, 605-610 (1979).
    • (1979) Biometrika , vol.66 , pp. 605-610
    • Scott, D.1
  • 56
    • 0029046703 scopus 로고
    • Order and coherence in the fate map of the zebrafish nervous system
    • Woo, K. & Fraser, S. E. Order and coherence in the fate map of the zebrafish nervous system. Development 121, 2595-2609 (1995).
    • (1995) Development , vol.121 , pp. 2595-2609
    • Woo, K.1    Fraser, S.E.2
  • 57
    • 78651430230 scopus 로고    scopus 로고
    • Control-free calling of copy number alterations in deepsequencing data using GC-content normalization
    • Boeva, V. et al. Control-free calling of copy number alterations in deepsequencing data using GC-content normalization. Bioinformatics 27, 268-269 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 268-269
    • Boeva, V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.