RNA-Seq analysis to capture the transcriptome landscape of a single cell (original) (raw)

• Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).
  Article CAS Google Scholar
• Cloonan, N. & Grimmond, S.M. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 9, 234 (2008).
  Article Google Scholar
• Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).
  Article CAS Google Scholar
• DeRisi, J. et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460 (1996).
  Article CAS Google Scholar
• Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 1675–1680 (1996).
  Article CAS Google Scholar
• Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P. & Trent, J.M. Expression profiling using cDNA microarrays. Nat. Genet. 21, 10–14 (1999).
  Article CAS Google Scholar
• Lipshutz, R.J., Fodor, S.P., Gingeras, T.R. & Lockhart, D.J. High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20–24 (1999).
  Article CAS Google Scholar
• Blackshaw, S. & Livesey, R. Applying genomics technologies to neural development. Curr. Opin. Neurobiol. 12, 110–114 (2002).
  Article CAS Google Scholar
• Royce, T.E. et al. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 21, 466–475 (2005).
  Article CAS Google Scholar
• Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851–1854 (2008).
  Article CAS Google Scholar
• Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133–141 (2008).
  Article CAS Google Scholar
• Wold, B. & Myers, R.M. Sequence census methods for functional genomics. Nat. Methods 5, 19–21 (2008).
  Article CAS Google Scholar
• Schuster, S.C. Next-generation sequencing transforms today′s biology. Nat. Methods 5, 16–18 (2008).
  Article CAS Google Scholar
• Shendure, J. The beginning of the end for microarrays? Nat. Methods 5, 585–587 (2008).
  Article CAS Google Scholar
• Wilhelm, B.T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008).
  Article CAS Google Scholar
• Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).
  Article CAS Google Scholar
• Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956–960 (2008).
  Article CAS Google Scholar
• Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).
  Article CAS Google Scholar
• Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613–619 (2008).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509–1517 (2008).
  Article CAS Google Scholar
• Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413–1415 (2008).
  Article CAS Google Scholar
• Li, H. et al. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc. Natl. Acad. Sci. USA. 105, 20179–20184 (2008).
  Article CAS Google Scholar
• Blake, W.J., Kærn, M., Cantor, C.R. & Collins, J.J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003).
  Article CAS Google Scholar
• Raser, J.M. & O′Shea, E.K. Noise in gene expression: origins, consequences, and control. Science 309, 2010–2013 (2005).
  Article CAS Google Scholar
• Arias, A.M. & Hayward, P. Filtering transcriptional noise during development: concepts and mechanisms. Nat. Rev. Genet. 7, 34–44 (2006).
  Article CAS Google Scholar
• Raj, A. & van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216–226 (2008).
  Article CAS Google Scholar
• Losick, R. & Desplan, C. Stochasticity and cell fate. Science 320, 65–68 (2008).
  Article CAS Google Scholar
• Shahrezaei, V. & Swain, P.S. The stochastic nature of biochemical networks. Curr. Opin. Biotechnol. 19, 369–374 (2008).
  Article CAS Google Scholar
• Kawasaki, E.S. Microarrays and the gene expression profile of a single cell. Ann. N Y Acad. Sci. 1020, 92–100 (2004).
  Article CAS Google Scholar
• Livesey, F.J. Strategies for microarray analysis of limiting amounts of RNA. Brief. Funct. Genomic Proteomic. 2, 31–36 (2003).
  Article CAS Google Scholar
• Hamatani, T., Carter, M.G., Sharov, A.A. & Ko, M.S. Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell 6, 117–131 (2004).
  Article CAS Google Scholar
• Wang, Q.T. et al. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev. Cell 6, 133–144 (2004).
  Article CAS Google Scholar
• Zeng, F., Baldwin, D.A. & Schultz, R.M. Transcript profiling during preimplantation mouse development. Dev. Biol. 272, 483–96 (2004).
  Article CAS Google Scholar
• Bontoux, N. et al. Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling. Lab Chip 8, 443–450 (2008).
  Article CAS Google Scholar
• Iscove, N.N. et al. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 20, 940–943 (2002).
  Article CAS Google Scholar
• Klein, C.A. et al. Combined transcriptome and genome analysis of single micrometastatic cells. Nat. Biotechnol. 20, 387–392 (2002).
  Article CAS Google Scholar
• Hartmann, C.H. & Klein, C.A. Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic Acids Res. 34, e143 (2006).
  Article Google Scholar
• Jensen, K.B. & Watt, F.M. Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence. Proc. Natl. Acad. Sci. USA 103, 11958–11963 (2006).
  Article CAS Google Scholar
• Kurimoto, K. et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res. 34, e42 (2006).
  Article Google Scholar
• 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. 2, 739–752 (2007).
  Article CAS Google Scholar
• Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).
  Article CAS Google Scholar
• Maekawa, M., Yamamoto, T., Kohno, M., Takeichi, M. & Nishida, E. Requirement for ERK MAP kinase in mouse preimplantation development. Development 134, 2751–2759 (2007).
  Article CAS Google Scholar
• Tang, F. et al. 220-plex microRNA expression profile of a single cell. Nat. Protoc. 1, 1154–1159 (2006).
  Article CAS Google Scholar
• Nagy, A., Gertsenstein, M., Vintersten, K. & Behringer, R. Manipulating the mouse embryo. 3rd ed., 194–200 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2003).
• Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230–1234 (2007).
  Article CAS Google Scholar
• Toyooka, Y., Shimosato, D., Murakami, K., Takahashi, K. & Niwa, H. Identification and characterization of subpopulations in undifferentiated ES cell culture. Development 135, 909–918 (2008).
  Article CAS Google Scholar
• 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 3, 391–401 (2008).
  Article CAS Google Scholar