Single-cell cDNA high-density oligonucleotide microarray analysis: Detection of individual cell types and properties in complex biological processes

Reproductive BioMedicine Online

Volumn 16, Issue 1, 2008, Pages 26-40

  Saitou, Mitinori ^a,b   Yabuta, Yukihiro ^a   Kurimoto, Kazuki ^a  

^a RIKEN KOBE INSTITUTE   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

Blastocyst; cDNA amplification; Cell fate specification; High density oligonucleotide microarray analysis; Single cells

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ANIMAL CELL; CELL ASSAY; CELL DIFFERENTIATION; CELL FATE; CELL MATURATION; CELL POPULATION; CELL STRUCTURE; CONFERENCE PAPER; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENOME ANALYSIS; INNER CELL MASS; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

EID: 38849122139     PISSN: 14726483     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1472-6483(10)60554-8     Document Type: Conference Paper

References (79)

1. Adams MD, Kelley JM, Gocayne JD et al. 1991 Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-1656.
2. Arman E, Haffner-Krausz R, Chen Y et al. 1998 Targeted disruption of fibroblast growth factor (FGF) receptor 2 suggests a role for FGF signaling in pregastrulation mammalian development. Proceedings of the National Academy of Sciences of the USA 95, 5082-5087.
3. Baugh LR, Hill AA, Slonim DK et al. 2003 Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development 130, 889-900.
4. Baugh LR, Hill AA, Brown EL et al. 2001 Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Research 29, E29.
5. Boguski MS, Lowe TM, Tolstoshev CM 1993 dbEST - database for 'expressed sequence tags'. Nature Genetics 4, 332-333.
6. Brady G, Iscove NN 1993 Construction of cDNA libraries from single cells. Methods in Enzymology 225, 611-623.
7. Brady G, Billia F, Knox J et al. 1995 Analysis of gene expression in a complex differentiation hierarchy by global amplification of cDNA from single cells. Current Biology 5, 909-922.
8. Brady G, Barbara M, Iscove N 1990 Representative in vitro cDNA amplification from individual hemopoietic cells and colonies. Methods in Molecular and Cellular Biology 2, 17-25.
9. Brail LH, Jang A, Billia F et al. 1999 Gene expression in individual cells: analysis using global single cell reverse transcription polymerase chain reaction (GSC RT-PCR). Mutation Research 406, 45-54.
10. Buck L, Axel R 1991 A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175-187.
11. Carter MG, Hamatani T, Sharov AA et al. 2003 In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expression profiling. Genome Research 13, 1011-1021.
12. Chazaud C, Rossant J 2006 Disruption of early proximodistal patterning and AVE formation in Apc mutants. Development 133, 3379-3387.
13. Chazaud C, Yamanaka Y, Pawson T et al. 2006 Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the Grb2 - MAPK pathway. Developmental Cell 10, 615-624.
14. Chiang MK, Melton DA 2003 Single-cell transcript analysis of pancreas development. Developmental Cell 4, 383-393.
15. Deng CX, Wynshaw-Boris A, Shen MM et al. 1994 Murine FGFR-1 is required for early postimplantation growth and axial organization. Genes and Development 8, 3045-3057.
16. Dulac C, Axel R 1995 A novel family of genes encoding putative pheromone receptors in mammals. Cell 83, 195-206.
17. Eberwine J 2001 Single-cell molecular biology. Nature Neuroscience 4 (Suppl.), 1155-1156.
18. Eberwine J, Yeh H, Miyashiro K et al. 1992 Analysis of gene expression in single live neurons. Proceedings of the National Academy of Sciences of the USA 89, 3010-3014.
19. Edwards RG, Hansis C 2005 Initial differentiation of blastomeres in 4-cell human embryos and its significance for early embryogenesis and implantation. Reproductive BioMedicine Online 11, 206-218.
20. Ensembl 2007 Release 46 http://www.ensembl.org/index.html [accessed 3 October 2007].
21. Feldman B, Poueymirou W, Papaioannou VE et al. 1995 Requirement of FGF-4 for postimplantation mouse development. Science 267, 246-249.
22. Gardner RL 2001 Specification of embryonic axes begins before cleavage in normal mouse development. Development 128, 839-847.
23. Gardner RL 1997 The early blastocyst is bilaterally symmetrical and its axis of symmetry is aligned with the animal - vegetal axis of the zygote in the mouse. Development 124, 299-301.
24. Ginsburg M, Snow MH, McLaren A 1990 Primordial germ cells in the mouse embryo during gastrulation. Development 110, 521-528.
25. Hamatani T, Carter MG, Sharov AA et al. 2004a Dynamics of global gene expression changes during mouse preimplantation development. Developmental Cell 6, 117-131.
26. Hamatani T, Daikoku T, Wang H et al. 2004b Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proceedings of the National Academy of Sciences of the USA 101, 10326-10331.
27. Hartmann CH, Klein CA 2006 Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic Acids Res 34, e143.
28. Heid CA, Stevens J, Livak KJ et al. 1996 Real time quantitative PCR. Genome Research 6, 986-994.
29. Higuchi R, Fockler C, Dollinger G et al. 1993 Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (NY) 11, 1026-1030.
30. Higuchi R, Dollinger G, Walsh PS et al. 1992 Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY) 10, 413-417.
31. Hiiragi T, Solter D 2004 First cleavage plane of the mouse egg is not predetermined but defined by the topology of the two apposing pronuclei. Nature 430, 360-364.
32. Iscove NN, Barbara M, Gu M et al. 2002 Representation is faithfully preserved in global cDNA amplified exponentially from subpicogram quantities of mRNA. Nature Biotechnology 20, 940-943.
33. Ji W, Zhou W, Gregg K et al. 2004 A method for gene expression analysis by oligonucleotide arrays from minute biological materials. Analytical Biochemistry 331, 329-339.
34. Johnson MH, McConnell JM 2004 Lineage allocation and cell polarity during mouse embryogenesis. Seminars in Cell and Developmental Biology 15, 583-597.
35. Johnson MH, Chisholm JC, Fleming TP et al. 1986 A role for cytoplasmic determinants in the development of the mouse early embryo? Journal of Embryology and Experimental Morphology 97 (Suppl.), 97-121.
36. Kamme F, Salunga R, Yu J et al. 2003 Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. Journal of Neuroscience 23, 3607-3615.
37. Klein CA, Seidl S, Petat-Dutter K et al. 2002 Combined transcriptome and genome analysis of single micrometastatic cells. Nature Biotechnology 20, 387-392.
38. Klur S, Toy K, Williams MP et al. 2004 Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics 83, 508-517.
39. Ko MS, Kitchen JR, Wang X et al. 2000 Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development 127, 1737-1749.
40. Ko MS, Ko SB, Takahashi N et al. 1990 Unbiased amplification of a highly complex mixture of DNA fragments by 'lone linker'-tagged PCR. Nucleic Acids Research 18, 4293-4294.
41. Kurimoto K, Yabuta Y, Ohinata Y et al. 2007 Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis. Nature Protocols 2, 739-752.
42. Kurimoto K, Yabuta Y, Ohinata Y et al. 2006 An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Research 34, e42.
43. Kurotaki Y, Hatta K, Nakao K et al. 2007 Blastocyst axis is specified independently of early cell lineage but aligns with the ZP shape. Science 316, 719-723.
44. Lipshutz RJ, Fodor SP, Gingeras TR et al. 1999 High density synthetic oligonucleotide arrays. Nature Genetics 21, 20-24.
45. Lockhart DJ, Dong H, Byrne MC et al. 1996 Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14, 1675-1680.
46. Louvet-Vallee S, Vinot S, Mato B 2005 Mitotic spindles and cleavage planes are oriented randomly in the two-cell mouse embryo. Current Biology 15, 464-469.
47. Marra M, Hillier L, Kucaba T et al. 1999 An encyclopedia of mouse genes. Nature Genetics 21, 191-194.
48. Matz M, Shagin D, Bogdanova E et al. 1999 Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Research 27, 1558-1560.
49. Motosugi N, Bauer T, Polanski Z et al. 2005 Polarity of the mouse embryo is established at blastocyst and is not prepatterned. Genes and Development 19, 1081-1092.
50. National Center for Biotechnology Information 2007 See http://www.ncbi.nlm.nih.gov [accessed 3 October 2007].
51. Niswander L, Martin GR 1992 Fgf-4 expression during gastrulation, myogenesis, limb and tooth development in the mouse, Development 114, 755-768.
52. Niwa H, Toyooka Y, Shimosato D et al. 2005 Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123, 917-929.
53. Ohinata Y, Payer B, O'Carroll D et al. 2005 Blimp1 is a critical determinant of the germ cell lineage in mice. Nature 436, 207-213.
54. Osawa M, Egawa G, Mak SS et al. 2005 Molecular characterization of melanocyte stem cells in their niche. Development 132, 5589-5599.
55. Petalidis L, Bhattacharyya S, Morris GA et al. 2003 Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Research 31, e142.
56. Piotrowska K, Zernicka-Goetz M 2001 Role for sperm in spatial patterning of the early mouse embryo. Nature 409, 517-521.
57. Piotrowska K, Wianny F, Pedersen RA et al. 2001 Blastomeres arising from the first cleavage division have distinguishable fates in normal mouse development. Development 128, 3739-3748.
58. Plusa B, Hadjantonakis AK, Gray D et al. 2005 The first cleavage of the mouse zygote predicts the blastocyst axis. Nature 434, 391-395.
59. Rappolee DA, Basilico C, Patel Y et al. 1994 Expression and function of FGF-4 in peri-implantation development in mouse embryos. Development 120, 2259-2269.
60. Rossant J 1976 Postimplantation development of blastomeres isolated from 4- and 8-cell mouse eggs. Journal of Embryology and Experimental Morphology 36, 283-290.
61. Saito H, Kubota M, Roberts RW et al. 2004 RTP family members induce functional expression of mammalian odorant receptors. Cell 119, 679-691.
62. Saitou M, Barton SC, Surani MA 2002 A molecular programme for the specification of germ cell fate in mice. Nature 418, 293-300.
63. Schena M, Shalon D, Davis RW et al. 1995 Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
64. Sen D, Gilbert W 1988 Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364-366.
65. Subkhankulova T, Livesey FJ 2006 Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level. Genome Biology 7, R18.
66. Sugino K, Hempel CM, Miller MN et al. 2006 Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nature Neuroscience 9, 99-107.
67. Surani MA, Hayashi K, Hajkova P 2007 Genetic and epigenetic regulators of pluripotency. Cell 128, 747-762.
68. Takaoka K, Yamamoto M, Shiratori H et al. 2006 The mouse embryo autonomously acquires anterior-posterior polarity at implantation. Developmental Cell 10, 451-459.
69. Tanabe Y, William C, Jessell TM 1998 Specification of motor neuron identity by the MNR2 homeodomain protein. Cell 95, 67-80.
70. Tarkowski AK 1961 Mouse chimaeras developed from fused eggs. Nature 190, 857-860.
71. Tarkowski AK 1959 Experiments on the development of isolated blastomeres of mouse eggs. Nature 184, 1286-1287.
72. Tarkowski AK, Wroblewska J 1967 Development of blastomeres of mouse eggs isolated at the 4- and 8-cell stage. Journal of Embryology and Experimental Morphology 18, 155-180.
73. Tietjen I, Rihel JM, Cao Y et al. 2003 Single-cell transcriptional analysis of neuronal progenitors. Neuron 38, 161-175.
74. Van Gelder RN, von Zastrow ME, Yool A et al. 1990 Amplified RNA synthesized from limited quantities of heterogeneous cDNA Proceedings of the National Academy of Sciences of the USA 87, 1663-1667.
75. Wilder PJ, Kelly D, Brigman K et al. 1997 Inactivation of the FGF-4 gene in embryonic stem cells alters the growth and/or the survival of their early differentiated progeny. Developmental Biology 192, 614-629.
76. Yabuta Y, Kurimoto K, Ohinata Y et al. 2006 Gene expression dynamics during germline specification in mice identified by quantitative single-cell gene expression profiling. Biology of Reproduction 75, 705-716.
77. Yamaguchi TP, Harpal K, Henkemeyer M et al. 1994 fgfr-1 is required for embryonic growth and mesodermal patterning during mouse gastrulation. Genes and Development 8, 3032-3044.
78. Yamamoto M, Saijoh Y, Perea-Gomez A et al. 2004 Nodal antagonists regulate formation of the anteroposterior axis of the mouse embryo. Nature 428, 387-392.
79. Zhu YY, Machleder EM, Chenchik A et al. 2001 Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30, 892-897.