메뉴 건너뛰기




Volumn 20, Issue 9, 2013, Pages 1131-1139

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; LONG UNTRANSLATED RNA; RNA; TRANSCRIPTOME;

EID: 84883743509     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2660     Document Type: Article
Times cited : (1291)

References (62)
  • 1
    • 82555169760 scopus 로고    scopus 로고
    • Gene expression heterogeneities in embryonic stem cell populations: Origin and function
    • Martinez Arias, A. & Brickman, J.M. Gene expression heterogeneities in embryonic stem cell populations: origin and function. Curr. Opin. Cell Biol. 23, 650-656 (2011).
    • (2011) Curr. Opin. Cell Biol , vol.23 , pp. 650-656
    • Martinez Arias, A.1    Brickman, J.M.2
  • 4
    • 80052266606 scopus 로고    scopus 로고
    • Non-invasive imaging of human embryos to predict developmental competence
    • Reijo Pera, R.A. Non-invasive imaging of human embryos to predict developmental competence. Placenta 32 (Suppl. 3), S264-S267 (2011).
    • (2011) Placenta , vol.32 , Issue.SUPPL. 3
    • Reijo Pera, R.A.1
  • 5
    • 84856946301 scopus 로고    scopus 로고
    • Comparative transcriptome analysis of human trophectoderm and embryonic stem cell-derived trophoblasts reveal key participants in early implantation
    • Aghajanova, L. et al. Comparative transcriptome analysis of human trophectoderm and embryonic stem cell-derived trophoblasts reveal key participants in early implantation. Biol. Reprod. 86, 1-21 (2012).
    • (2012) Biol. Reprod , vol.86 , pp. 1-21
    • Aghajanova, L.1
  • 6
    • 79951743841 scopus 로고    scopus 로고
    • Dynamic changes in gene expression during human early embryo development: From fundamental aspects to clinical applications
    • Assou, S. et al. Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum. Reprod. Update 17, 272-290 (2011).
    • (2011) Hum. Reprod. Update , vol.17 , pp. 272-290
    • Assou, S.1
  • 7
    • 84862686733 scopus 로고    scopus 로고
    • Transcriptome analysis during human trophectoderm specification suggests new roles of metabolic and epigenetic genes
    • Assou, S. et al. Transcriptome analysis during human trophectoderm specification suggests new roles of metabolic and epigenetic genes. PLoS ONE 7, e39306 (2012).
    • (2012) PLoS ONE , vol.7
    • Assou, S.1
  • 8
    • 58849123232 scopus 로고    scopus 로고
    • A gene expression signature shared by human mature oocytes and embryonic stem cells
    • Assou, S. et al. A gene expression signature shared by human mature oocytes and embryonic stem cells. BMC Genomics 10, 10 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 10
    • Assou, S.1
  • 9
    • 84857658568 scopus 로고    scopus 로고
    • Dissecting the first transcriptional divergence during human embryonic development
    • Bai, Q. et al. Dissecting the first transcriptional divergence during human embryonic development. Stem Cell Rev. Rep. 8, 150-162 (2012).
    • (2012) Stem Cell Rev. Rep , vol.8 , pp. 150-162
    • Bai, Q.1
  • 11
    • 78149430467 scopus 로고    scopus 로고
    • Functional genomics of 5-to 8-cell stage human embryos by blastomere single-cell cDNA analysis
    • Gal?, A. et al. Functional genomics of 5-to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PLoS ONE 5, e13615 (2010).
    • (2010) PLoS ONE , vol.5
    • Gal, A.1
  • 12
    • 79957506214 scopus 로고    scopus 로고
    • Transcriptome analysis reveals dialogues between human trophectoderm and endometrial cells during the implantation period
    • Haouzi, D. et al. Transcriptome analysis reveals dialogues between human trophectoderm and endometrial cells during the implantation period. Hum. Reprod. 26, 1440-1449 (2011).
    • (2011) Hum. Reprod , vol.26 , pp. 1440-1449
    • Haouzi, D.1
  • 13
    • 80051493701 scopus 로고    scopus 로고
    • Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development
    • Vassena, R. et al. Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development. Development 138, 3699-3709 (2011).
    • (2011) Development , vol.138 , pp. 3699-3709
    • Vassena, R.1
  • 14
    • 77957938684 scopus 로고    scopus 로고
    • Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage
    • Wong, C.C. et al. Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage. Nat. Biotechnol. 28, 1115-1121 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 1115-1121
    • Wong, C.C.1
  • 15
    • 77952962147 scopus 로고    scopus 로고
    • Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
    • Xie, D. et al. Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res. 20, 804-815 (2010).
    • (2010) Genome Res , vol.20 , pp. 804-815
    • Xie, D.1
  • 16
    • 67349223575 scopus 로고    scopus 로고
    • Evidence that human blastomere cleavage is under unique cell cycle control
    • Kiessling, A.A. et al. Evidence that human blastomere cleavage is under unique cell cycle control. J. Assist. Reprod. Genet. 26, 187-195 (2009).
    • (2009) J. Assist. Reprod. Genet , vol.26 , pp. 187-195
    • Kiessling, A.A.1
  • 17
    • 77956490803 scopus 로고    scopus 로고
    • Genome-wide microarray evidence that 8-cell human blastomeres over-express cell cycle drivers and under-express checkpoints
    • Kiessling, A.A. et al. Genome-wide microarray evidence that 8-cell human blastomeres over-express cell cycle drivers and under-express checkpoints. J. Assist. Reprod. Genet. 27, 265-276 (2010).
    • (2010) J. Assist. Reprod. Genet , vol.27 , pp. 265-276
    • Kiessling, A.A.1
  • 18
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman, M. & Rinn, J.L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346 (2012).
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 19
    • 0032491416 scopus 로고    scopus 로고
    • Embryonic stem cell lines derived from human blastocysts
    • Thomson, J.A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145-1147 (1998). (Pubitemid 28516247)
    • (1998) Science , vol.282 , Issue.5391 , pp. 1145-1147
    • Thomson, J.A.1
  • 20
    • 67649392297 scopus 로고    scopus 로고
    • Gene expression profiles of human inner cell mass cells and embryonic stem cells
    • Reijo Pera, R.A. et al. Gene expression profiles of human inner cell mass cells and embryonic stem cells. Differentiation 78, 18-23 (2009).
    • (2009) Differentiation , vol.78 , pp. 18-23
    • Reijo Pera, R.A.1
  • 21
    • 84857991080 scopus 로고    scopus 로고
    • Tracking the progression of the human inner cell mass during embryonic stem cell derivation
    • O'Leary, T. et al. Tracking the progression of the human inner cell mass during embryonic stem cell derivation. Nat. Biotechnol. 30, 278-282 (2012).
    • (2012) Nat. Biotechnol , vol.30 , pp. 278-282
    • O'Leary, T.1
  • 22
    • 67349146589 scopus 로고    scopus 로고
    • MRNA-Seq whole-transcriptome analysis of a single cell
    • Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 377-382
    • Tang, F.1
  • 23
    • 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 8, S6-S11 (2011).
    • (2011) Nat. Methods , vol.8
    • Tang, F.1    Lao, K.2    Surani, M.A.3
  • 24
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
    • Ramsk?d, 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
    • Ramskd, D.1
  • 25
    • 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
  • 26
    • 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. et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6, 468-478 (2010).
    • (2010) Cell Stem Cell , vol.6 , pp. 468-478
    • Tang, F.1
  • 27
    • 0023874053 scopus 로고
    • Human gene expression first occurs between the four- and eight-cell stages of preimplantation development
    • DOI 10.1038/332459a0
    • Braude, P., Bolton, V. & Moore, S. Human gene expression first occurs between the four-and eight-cell stages of preimplantation development. Nature 332, 459-461 (1988). (Pubitemid 18090251)
    • (1988) Nature , vol.332 , Issue.6163 , pp. 459-461
    • Braude, P.1    Bolton, V.2    Moore, S.3
  • 28
    • 77951171043 scopus 로고    scopus 로고
    • Making the blastocyst: Lessons from the mouse
    • Cockburn, K. & Rossant, J. Making the blastocyst: lessons from the mouse. J. Clin. Invest. 120, 995-1003 (2010).
    • (2010) J. Clin. Invest , vol.120 , pp. 995-1003
    • Cockburn, K.1    Rossant, J.2
  • 29
    • 65549115574 scopus 로고    scopus 로고
    • Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse
    • Rossant, J. & Tam, P.P.L. Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Development 136, 701-713 (2009).
    • (2009) Development , vol.136 , pp. 701-713
    • Rossant, J.1    Tam, P.P.L.2
  • 30
    • 80052223272 scopus 로고    scopus 로고
    • An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming
    • Gabut, M. et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 147, 132-146 (2011).
    • (2011) Cell , vol.147 , pp. 132-146
    • Gabut, M.1
  • 31
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667-11672 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 11667-11672
    • Khalil, A.M.1
  • 32
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • Rom, U.A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46-58 (2010).
    • (2010) Cell , vol.143 , pp. 46-58
    • Rom, U.A.1
  • 33
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • Wang, K.C. & Chang, H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914 (2011).
    • (2011) Mol. Cell , vol.43 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 34
    • 80052869283 scopus 로고    scopus 로고
    • LincRNAs act in the circuitry controlling pluripotency and differentiation
    • Guttman, M. et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295-300 (2011).
    • (2011) Nature , vol.477 , pp. 295-300
    • Guttman, M.1
  • 35
    • 84861202972 scopus 로고    scopus 로고
    • The long non-coding RNAs (lncRNAs): A new (p) layer in the dark matter
    • Derrien, T., Guig? R. & Johnson, R. The long non-coding RNAs (lncRNAs): a new (p) layer in the "dark matter". Frontiers Genet. 2, 107 (2012).
    • (2012) Frontiers Genet , vol.2 , pp. 107
    • Derrien, T.1    Guig, R.2    Johnson, R.3
  • 36
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 37
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong, L. et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345-9 (2007).
    • (2007) Nucleic Acids Res , vol.35
    • Kong, L.1
  • 38
    • 66349086264 scopus 로고    scopus 로고
    • Identifying novel constrained elements by exploiting biased substitution patterns
    • Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25, i54-i62 (2009).
    • (2009) Bioinformatics , vol.25
    • Garber, M.1
  • 39
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
    • Guttman, M. et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1
  • 40
    • 41349099021 scopus 로고    scopus 로고
    • Gene expression profiling of human oocytes at different maturational stages and after in vitro maturation
    • Wells, D. & Patrizio, P. Gene expression profiling of human oocytes at different maturational stages and after in vitro maturation. Am. J. Obstet. Gynecol. 198, 455.e1-455. e11 (2008).
    • (2008) Am. J. Obstet. Gynecol , vol.198
    • Wells, D.1    Patrizio, P.2
  • 41
    • 84355166507 scopus 로고    scopus 로고
    • Human hypoblast formation is not dependent on FGF signalling
    • Roode, M. et al. Human hypoblast formation is not dependent on FGF signalling. Dev. Biol. 361, 358-363 (2012).
    • (2012) Dev. Biol , vol.361 , pp. 358-363
    • Roode, M.1
  • 42
    • 34447527158 scopus 로고    scopus 로고
    • Derivation of pluripotent epiblast stem cells from mammalian embryos
    • DOI 10.1038/nature05950, PII NATURE05950
    • Brons, I.G.M. et al. Derivation of pluripotent epiblast stem cells from mammalian embryos. Nature 448, 191-195 (2007). (Pubitemid 47067373)
    • (2007) Nature , vol.448 , Issue.7150 , pp. 191-195
    • Brons, I.G.M.1
  • 45
    • 33745612095 scopus 로고    scopus 로고
    • Pvclust: An R package for assessing the uncertainty in hierarchical clustering
    • DOI 10.1093/bioinformatics/btl117
    • Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540-1542 (2006). (Pubitemid 43985330)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1540-1542
    • Suzuki, R.1    Shimodaira, H.2
  • 46
    • 72149107557 scopus 로고    scopus 로고
    • Characteristics of embryo development in Robertsonian translocations' preimplantation genetic diagnosis cycles
    • Huang, J. et al. Characteristics of embryo development in Robertsonian translocations' preimplantation genetic diagnosis cycles. Prenat. Diagn. 29, 1167-1170 (2009).
    • (2009) Prenat. Diagn , vol.29 , pp. 1167-1170
    • Huang, J.1
  • 47
    • 77749323185 scopus 로고    scopus 로고
    • RNA-seq analysis to capture the transcriptome landscape of a single cell
    • Tang, F. et al. RNA-seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 5, 516-535 (2010).
    • (2010) Nat. Protoc , vol.5 , pp. 516-535
    • Tang, F.1
  • 48
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 49
    • 84860742355 scopus 로고    scopus 로고
    • NONCODE v3.0: Integrative annotation of long noncoding RNAs
    • Bu, D. et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. D210-5 (2012).
    • (2012) Nucleic Acids Res , vol.D210-5
    • Bu, D.1
  • 50
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M.G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 52
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The blast-like alignment tool
    • Kent, W.J. BLAT-The BLAST-Like Alignment Tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 53
    • 16644377422 scopus 로고    scopus 로고
    • Methods of embryo scoring in in vitro fertilization
    • Baczkowski, T., Kurzawa, R. & Glabowski, W. Methods of embryo scoring in in vitro fertilization. Reprod. Biol. 4, 5-22 (2004).
    • (2004) Reprod. Biol , vol.4 , pp. 5-22
    • Baczkowski, T.1    Kurzawa, R.2    Glabowski, W.3
  • 54
    • 34249708977 scopus 로고    scopus 로고
    • Na/K-ATPase β1 subunit expression is required for blastocyst formation and normal assembly of trophectoderm tight junction-associated proteins
    • DOI 10.1074/jbc.M700696200
    • Madan, P., Rose, K. & Watson, A.J. Na/K-ATPase ?1 subunit expression is required for blastocyst formation and normal assembly of trophectoderm tight junction-associated proteins. J. Biol. Chem. 282, 12127-12134 (2007). (Pubitemid 47100727)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.16 , pp. 12127-12134
    • Madan, P.1    Rose, K.2    Watson, A.J.3
  • 55
    • 77951912210 scopus 로고    scopus 로고
    • Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst
    • Guo, G. et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev. Cell 18, 675-685 (2010).
    • (2010) Dev. Cell , vol.18 , pp. 675-685
    • Guo, G.1
  • 56
    • 70350627509 scopus 로고    scopus 로고
    • Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells
    • Bao, S. et al. Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells. Nature 461, 1292-1295 (2009).
    • (2009) Nature , vol.461 , pp. 1292-1295
    • Bao, S.1
  • 57
    • 0030681260 scopus 로고    scopus 로고
    • The significance of digital gene expression profiles
    • Audic, S.p. & Claverie, J.-M. The significance of digital gene expression profiles. Genome Res. 7, 986-995 (1997). (Pubitemid 27487763)
    • (1997) Genome Research , vol.7 , Issue.10 , pp. 986-995
    • Audic, S.1    Claverie, J.-M.2
  • 58
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008). (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 60
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview - Extensible visualization of microarray data
    • DOI 10.1093/bioinformatics/bth349
    • Saldanha, A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248 (2004). (Pubitemid 39619217)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3246-3248
    • Saldanha, A.J.1
  • 61
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B 57, 289-300 (1995).
    • (1995) J. Roy. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 62
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2008).
    • (2008) Nat. Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.