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Volumn 24, Issue 1, 2013, Pages 69-78

Investigating transcriptional states at single-cell-resolution

Author keywords

[No Author keywords available]

Indexed keywords

CELL POPULATIONS; CELL STATE; COMPLEX TISSUES; DISEASE DEVELOPMENT; GENE EXPRESSION ANALYSIS; GENETIC REGULATORY CIRCUITS; INDIVIDUAL CELLS; MOLECULAR BASIS; MOLECULAR CELLS; PERSONALIZED MEDICINES;

EID: 84872264658     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2012.09.013     Document Type: Review
Times cited : (30)

References (71)
  • 1
    • 70450162700 scopus 로고    scopus 로고
    • Non-genetic heterogeneity of cells in development: more than just noise
    • Huang S. Non-genetic heterogeneity of cells in development: more than just noise. Development 2009, 136:3853-3862.
    • (2009) Development , vol.136 , pp. 3853-3862
    • Huang, S.1
  • 2
    • 79960630264 scopus 로고    scopus 로고
    • Central dogma at the single-molecule level in living cells
    • Li G.W., Xie X.S. Central dogma at the single-molecule level in living cells. Nature 2011, 475:308-315.
    • (2011) Nature , vol.475 , pp. 308-315
    • Li, G.W.1    Xie, X.S.2
  • 3
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: stochastic gene expression and its consequences
    • Raj A., van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008, 135:216-226.
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    van Oudenaarden, A.2
  • 4
    • 79952638264 scopus 로고    scopus 로고
    • Cellular decision making and biological noise: from microbes to mammals
    • Balazsi G., van Oudenaarden A., Collins J.J. Cellular decision making and biological noise: from microbes to mammals. Cell 2011, 144:910-925.
    • (2011) Cell , vol.144 , pp. 910-925
    • Balazsi, G.1    van Oudenaarden, A.2    Collins, J.J.3
  • 5
    • 77956520011 scopus 로고    scopus 로고
    • Functional roles for noise in genetic circuits
    • Eldar A., Elowitz M.B. Functional roles for noise in genetic circuits. Nature 2010, 467:167-173.
    • (2010) Nature , vol.467 , pp. 167-173
    • Eldar, A.1    Elowitz, M.B.2
  • 6
    • 77956892318 scopus 로고    scopus 로고
    • The role of physiological heterogeneity in microbial population behavior
    • Lidstrom M.E., Konopka M.C. The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol 2010, 6:705-712.
    • (2010) Nat Chem Biol , vol.6 , pp. 705-712
    • Lidstrom, M.E.1    Konopka, M.C.2
  • 7
    • 78951470515 scopus 로고    scopus 로고
    • Origins of regulated cell-to-cell variability
    • Snijder B., Pelkmans L. Origins of regulated cell-to-cell variability. Nat Rev Mol Cell Biol 2011, 12:119-125.
    • (2011) Nat Rev Mol Cell Biol , vol.12 , pp. 119-125
    • Snijder, B.1    Pelkmans, L.2
  • 8
    • 77952915049 scopus 로고    scopus 로고
    • Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript
    • Canham M.A., Sharov A.A., Ko M.S., Brickman J.M. Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript. PLoS Biol 2010, 8:e1000379.
    • (2010) PLoS Biol , vol.8
    • Canham, M.A.1    Sharov, A.A.2    Ko, M.S.3    Brickman, J.M.4
  • 11
    • 53049092465 scopus 로고    scopus 로고
    • Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states
    • Hayashi K., Lopes S.M., Tang F., Surani M.A. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell 2008, 3:391-401.
    • (2008) Cell Stem Cell , vol.3 , pp. 391-401
    • Hayashi, K.1    Lopes, S.M.2    Tang, F.3    Surani, M.A.4
  • 13
    • 69249215528 scopus 로고    scopus 로고
    • The cyclic gene hes1 contributes to diverse differentiation responses of embryonic stem cells
    • Kobayashi T., Mizuno H., Imayoshi I., Furusawa C., Shirahige K., Kageyama R. The cyclic gene hes1 contributes to diverse differentiation responses of embryonic stem cells. Genes Dev 2009, 23:1870-1875.
    • (2009) Genes Dev , vol.23 , pp. 1870-1875
    • Kobayashi, T.1    Mizuno, H.2    Imayoshi, I.3    Furusawa, C.4    Shirahige, K.5    Kageyama, R.6
  • 15
    • 42149192008 scopus 로고    scopus 로고
    • Identification and characterization of subpopulations in undifferentiated es cell culture
    • Toyooka Y., Shimosato D., Murakami K., Takahashi K., Niwa H. Identification and characterization of subpopulations in undifferentiated es cell culture. Development 2008, 135:909-918.
    • (2008) Development , vol.135 , pp. 909-918
    • Toyooka, Y.1    Shimosato, D.2    Murakami, K.3    Takahashi, K.4    Niwa, H.5
  • 16
    • 44349162752 scopus 로고    scopus 로고
    • Transcriptome-wide noise controls lineage choice in mammalian progenitor cells
    • Chang H.H., Hemberg M., Barahona M., Ingber D.E., Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 2008, 453:544-547.
    • (2008) Nature , vol.453 , pp. 544-547
    • Chang, H.H.1    Hemberg, M.2    Barahona, M.3    Ingber, D.E.4    Huang, S.5
  • 17
    • 33646527782 scopus 로고    scopus 로고
    • Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the grb2-mapk pathway
    • Chazaud C., Yamanaka Y., Pawson T., Rossant J. Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the grb2-mapk pathway. Dev Cell 2006, 10:615-624.
    • (2006) Dev Cell , vol.10 , pp. 615-624
    • Chazaud, C.1    Yamanaka, Y.2    Pawson, T.3    Rossant, J.4
  • 18
    • 38049095768 scopus 로고    scopus 로고
    • Stochastic patterning in the mouse pre-implantation embryo
    • Dietrich J.E., Hiiragi T. Stochastic patterning in the mouse pre-implantation embryo. Development 2007, 134:4219-4231.
    • (2007) Development , vol.134 , pp. 4219-4231
    • Dietrich, J.E.1    Hiiragi, T.2
  • 19
    • 77951912210 scopus 로고    scopus 로고
    • Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst
    • Guo G., Huss M., Tong G.Q., Wang C., Li Sun L., Clarke N.D., Robson P. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell 2010, 18:675-685.
    • (2010) Dev Cell , vol.18 , pp. 675-685
    • Guo, G.1    Huss, M.2    Tong, G.Q.3    Wang, C.4    Li Sun, L.5    Clarke, N.D.6    Robson, P.7
  • 20
    • 65549115574 scopus 로고    scopus 로고
    • Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse
    • Rossant J., Tam P.P. Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Development 2009, 136:701-713.
    • (2009) Development , vol.136 , pp. 701-713
    • Rossant, J.1    Tam, P.P.2
  • 23
    • 84859113048 scopus 로고    scopus 로고
    • Genetic heterogeneity and cancer drug resistance
    • Turner N.C., Reis-Filho J.S. Genetic heterogeneity and cancer drug resistance. Lancet Oncol 2012, 13:e178-e185.
    • (2012) Lancet Oncol , vol.13
    • Turner, N.C.1    Reis-Filho, J.S.2
  • 24
    • 84856468378 scopus 로고    scopus 로고
    • Microfluidics for single cell analysis
    • Yin H., Marshall D. Microfluidics for single cell analysis. Curr Opin Biotechnol 2012, 23:110-119.
    • (2012) Curr Opin Biotechnol , vol.23 , pp. 110-119
    • Yin, H.1    Marshall, D.2
  • 25
    • 77956412152 scopus 로고    scopus 로고
    • Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell rna-seq analysis
    • Tang F., Barbacioru C., Bao S., Lee C., Nordman E., Wang X., Lao K., Surani M.A. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell rna-seq analysis. Cell Stem Cell 2010, 6:468-478.
    • (2010) Cell Stem Cell , vol.6 , pp. 468-478
    • Tang, F.1    Barbacioru, C.2    Bao, S.3    Lee, C.4    Nordman, E.5    Wang, X.6    Lao, K.7    Surani, M.A.8
  • 28
    • 79953288433 scopus 로고    scopus 로고
    • Development and applications of single-cell transcriptome analysis
    • Tang F., Lao K., Surani M.A. Development and applications of single-cell transcriptome analysis. Nat Methods 2011, 8(4 Suppl.):S6-S11.
    • (2011) Nat Methods , vol.8 , Issue.4 SUPPL.
    • Tang, F.1    Lao, K.2    Surani, M.A.3
  • 30
    • 34347235153 scopus 로고    scopus 로고
    • Global single-cell cdna amplification to provide a template for representative high-density oligonucleotide microarray analysis
    • Kurimoto K., Yabuta Y., Ohinata Y., Saitou M. Global single-cell cdna amplification to provide a template for representative high-density oligonucleotide microarray analysis. Nat Protoc 2007, 2:739-752.
    • (2007) Nat Protoc , vol.2 , pp. 739-752
    • Kurimoto, K.1    Yabuta, Y.2    Ohinata, Y.3    Saitou, M.4
  • 32
    • 34347256054 scopus 로고    scopus 로고
    • Microfluidic large-scale integration: the evolution of design rules for biological automation
    • Melin J., Quake S.R. Microfluidic large-scale integration: the evolution of design rules for biological automation. Annu Rev Biophys Biomol Struct 2007, 36:213-231.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 213-231
    • Melin, J.1    Quake, S.R.2
  • 33
    • 0034908917 scopus 로고    scopus 로고
    • Microfluidics - downsizing large-scale biology
    • Mitchell P. Microfluidics - downsizing large-scale biology. Nat Biotechnol 2001, 19:717-721.
    • (2001) Nat Biotechnol , vol.19 , pp. 717-721
    • Mitchell, P.1
  • 34
    • 33747117373 scopus 로고    scopus 로고
    • The origins and the future of microfluidics
    • Whitesides G.M. The origins and the future of microfluidics. Nature 2006, 442:368-373.
    • (2006) Nature , vol.442 , pp. 368-373
    • Whitesides, G.M.1
  • 35
    • 0141816971 scopus 로고    scopus 로고
    • Solving the " world-to-chip" interface problem with a microfluidic matrix
    • Liu J., Hansen C., Quake S.R. Solving the " world-to-chip" interface problem with a microfluidic matrix. Anal Chem 2003, 75:4718-4723.
    • (2003) Anal Chem , vol.75 , pp. 4718-4723
    • Liu, J.1    Hansen, C.2    Quake, S.R.3
  • 36
    • 45849087630 scopus 로고    scopus 로고
    • High throughput gene expression measurement with real time pcr in a microfluidic dynamic array
    • Spurgeon S.L., Jones R.C., Ramakrishnan R. High throughput gene expression measurement with real time pcr in a microfluidic dynamic array. PLoS ONE 2008, 3:e1662.
    • (2008) PLoS ONE , vol.3
    • Spurgeon, S.L.1    Jones, R.C.2    Ramakrishnan, R.3
  • 37
    • 33845218548 scopus 로고    scopus 로고
    • Transcription factor profiling in individual hematopoietic progenitors by digital rt-pcr
    • Warren L., Bryder D., Weissman I.L., Quake S.R. Transcription factor profiling in individual hematopoietic progenitors by digital rt-pcr. Proc Natl Acad Sci USA 2006, 103:17807-17812.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17807-17812
    • Warren, L.1    Bryder, D.2    Weissman, I.L.3    Quake, S.R.4
  • 39
    • 84859602728 scopus 로고    scopus 로고
    • Microfluidic single-cell real-time pcr for comparative analysis of gene expression patterns
    • Sanchez-Freire V., Ebert A.D., Kalisky T., Quake S.R., Wu J.C. Microfluidic single-cell real-time pcr for comparative analysis of gene expression patterns. Nat Protoc 2012, 7:829-838.
    • (2012) Nat Protoc , vol.7 , pp. 829-838
    • Sanchez-Freire, V.1    Ebert, A.D.2    Kalisky, T.3    Quake, S.R.4    Wu, J.C.5
  • 42
    • 79953273690 scopus 로고    scopus 로고
    • Validating transcripts with probes and imaging technology
    • Itzkovitz S., van Oudenaarden A. Validating transcripts with probes and imaging technology. Nat Methods 2011, 8(4 Suppl.):S12-S19.
    • (2011) Nat Methods , vol.8 , Issue.4 SUPPL.
    • Itzkovitz, S.1    van Oudenaarden, A.2
  • 43
    • 0032562720 scopus 로고    scopus 로고
    • Visualization of single rna transcripts in situ
    • Femino A.M., Fay F.S., Fogarty K., Singer R.H. Visualization of single rna transcripts in situ. Science 1998, 280:585-590.
    • (1998) Science , vol.280 , pp. 585-590
    • Femino, A.M.1    Fay, F.S.2    Fogarty, K.3    Singer, R.H.4
  • 48
    • 77952243279 scopus 로고    scopus 로고
    • In situ detection and genotyping of individual mrna molecules
    • Larsson C., Grundberg I., Soderberg O., Nilsson M. In situ detection and genotyping of individual mrna molecules. Nat Methods 2010, 7:395-397.
    • (2010) Nat Methods , vol.7 , pp. 395-397
    • Larsson, C.1    Grundberg, I.2    Soderberg, O.3    Nilsson, M.4
  • 49
    • 69049086730 scopus 로고    scopus 로고
    • Imaging individual micrornas in single mammalian cells in situ
    • Lu J., Tsourkas A. Imaging individual micrornas in single mammalian cells in situ. Nucleic Acids Res 2009, 37:e100.
    • (2009) Nucleic Acids Res , vol.37
    • Lu, J.1    Tsourkas, A.2
  • 52
    • 84857395611 scopus 로고    scopus 로고
    • Single-cell analysis reveals that noncoding rnas contribute to clonal heterogeneity by modulating transcription factor recruitment
    • Bumgarner S.L., Neuert G., Voight B.F., Symbor-Nagrabska A., Grisafi P., van Oudenaarden A., Fink G.R. Single-cell analysis reveals that noncoding rnas contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell 2012, 45:470-482.
    • (2012) Mol Cell , vol.45 , pp. 470-482
    • Bumgarner, S.L.1    Neuert, G.2    Voight, B.F.3    Symbor-Nagrabska, A.4    Grisafi, P.5    van Oudenaarden, A.6    Fink, G.R.7
  • 53
    • 84859641038 scopus 로고    scopus 로고
    • Using gene expression noise to understand gene regulation
    • Munsky B., Neuert G., van Oudenaarden A. Using gene expression noise to understand gene regulation. Science 2012, 336:183-187.
    • (2012) Science , vol.336 , pp. 183-187
    • Munsky, B.1    Neuert, G.2    van Oudenaarden, A.3
  • 54
    • 64749116742 scopus 로고    scopus 로고
    • Using movies to analyse gene circuit dynamics in single cells
    • Locke J.C., Elowitz M.B. Using movies to analyse gene circuit dynamics in single cells. Nat Rev Microbiol 2009, 7:383-392.
    • (2009) Nat Rev Microbiol , vol.7 , pp. 383-392
    • Locke, J.C.1    Elowitz, M.B.2
  • 55
    • 79953280811 scopus 로고    scopus 로고
    • Long-term single-cell imaging of mammalian stem cells
    • Schroeder T. Long-term single-cell imaging of mammalian stem cells. Nat Methods 2011, 8(4 Suppl.):S30-S35.
    • (2011) Nat Methods , vol.8 , Issue.4 SUPPL.
    • Schroeder, T.1
  • 59
    • 80755168360 scopus 로고    scopus 로고
    • Genomic analysis at the single-cell level
    • Kalisky T., Blainey P., Quake S.R. Genomic analysis at the single-cell level. Annu Rev Genet 2011, 45:431-445.
    • (2011) Annu Rev Genet , vol.45 , pp. 431-445
    • Kalisky, T.1    Blainey, P.2    Quake, S.R.3
  • 60
    • 15544388848 scopus 로고    scopus 로고
    • Noise propagation in gene networks
    • Pedraza J.M., van Oudenaarden A. Noise propagation in gene networks. Science 2005, 307:1965-1969.
    • (2005) Science , vol.307 , pp. 1965-1969
    • Pedraza, J.M.1    van Oudenaarden, A.2
  • 62
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao C.V., Wolf D.M., Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:231-237.
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.V.1    Wolf, D.M.2    Arkin, A.P.3
  • 63
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser J.M., O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 2004, 304:1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 65
    • 33645027986 scopus 로고    scopus 로고
    • Stochastic protein expression in individual cells at the single molecule level
    • Cai L., Friedman N., Xie X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 2006, 440:358-362.
    • (2006) Nature , vol.440 , pp. 358-362
    • Cai, L.1    Friedman, N.2    Xie, X.S.3
  • 66
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    • Taniguchi Y., Choi P.J., Li G.W., Chen H., Babu M., Hearn J., Emili A., Xie X.S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538.
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.W.3    Chen, H.4    Babu, M.5    Hearn, J.6    Emili, A.7    Xie, X.S.8
  • 67
    • 78649675624 scopus 로고    scopus 로고
    • Evaluating gene expression dynamics using pairwise rna fish data
    • Wyart M., Botstein D., Wingreen N.S. Evaluating gene expression dynamics using pairwise rna fish data. PLoS Comput Biol 2010, 6:e1000979.
    • (2010) PLoS Comput Biol , vol.6
    • Wyart, M.1    Botstein, D.2    Wingreen, N.S.3
  • 69
    • 44949231424 scopus 로고    scopus 로고
    • Analyzing real-time pcr data by the comparative c(t) method
    • Schmittgen T.D., Livak K.J. Analyzing real-time pcr data by the comparative c(t) method. Nat Protoc 2008, 3:1101-1108.
    • (2008) Nat Protoc , vol.3 , pp. 1101-1108
    • Schmittgen, T.D.1    Livak, K.J.2
  • 70
    • 65249141709 scopus 로고    scopus 로고
    • Database for mrna half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
    • Sharova L.V., Sharov A.A., Nedorezov T., Piao Y., Shaik N., Ko M.S. Database for mrna half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res 2009, 16:45-58.
    • (2009) DNA Res , vol.16 , pp. 45-58
    • Sharova, L.V.1    Sharov, A.A.2    Nedorezov, T.3    Piao, Y.4    Shaik, N.5    Ko, M.S.6
  • 71
    • 67650762824 scopus 로고    scopus 로고
    • Super-resolution fluorescence microscopy
    • Huang B., Bates M., Zhuang X. Super-resolution fluorescence microscopy. Annu Rev Biochem 2009, 78:993-1016.
    • (2009) Annu Rev Biochem , vol.78 , pp. 993-1016
    • Huang, B.1    Bates, M.2    Zhuang, X.3


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