Integrated genome and transcriptome sequencing of the same cell (original) (raw)

• Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848–853 (2007).
  Article CAS Google Scholar
• Conrad, D.F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010).
  Article CAS Google Scholar
• Keane, T.M. et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289–294 (2011).
  Article CAS Google Scholar
• Sheltzer, J.M., Torres, E.M., Dunham, M.J. & Amon, A. Transcriptional consequences of aneuploidy. Proc. Natl. Acad. Sci. USA 109, 12644–12649 (2012).
  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
• Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90–94 (2011).
  Article CAS Google Scholar
• Zong, C., Lu, S., Chapman, A.R. & Xie, X.S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338, 1622–1626 (2012).
  Article CAS Google Scholar
• Falconer, E. et al. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat. Methods 9, 1107–1112 (2012).
  Article CAS Google Scholar
• Hou, Y. et al. Genome analyses of single human oocytes. Cell 155, 1492–1506 (2013).
  Article CAS Google Scholar
• Evrony, G.D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483–496 (2012).
  Article CAS Google Scholar
• McConnell, M.J. et al. Mosaic copy number variation in human neurons. Science 342, 632–637 (2013).
  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
• Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Reports 2, 666–673 (2012).
  Article CAS Google Scholar
• Shalek, A.K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236–240 (2013).
  Article CAS Google Scholar
• Xue, Z. et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500, 593–597 (2013).
  Article CAS Google Scholar
• Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096–1098 (2013).
  Article CAS Google Scholar
• Islam, S. et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11, 163–166 (2014).
  Article CAS Google Scholar
• Wu, A.R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11, 41–46 (2014).
  Article CAS Google Scholar
• Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193–196 (2014).
  Article CAS Google Scholar
• Jaitin, D.A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–779 (2014).
  Article CAS Google Scholar
• Grün, D., Kester, L. & van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat. Methods 11, 637–640 (2014).
  Article Google Scholar
• Junker, J.P. & van Oudenaarden, A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell 157, 8–11 (2014).
  Article CAS Google Scholar
• Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618–630 (2013).
  Article CAS Google Scholar
• Baker, S.C. et al. The External RNA Controls Consortium. A progress report. Nat. Methods 2, 731–734 (2005).
  Article CAS Google Scholar
• Zhang, C. et al. A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing. PLoS ONE 8, e54236 (2013).
  Article CAS Google Scholar
• Venkatraman, E.S. & Olshen, A.B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007).
  Article CAS Google Scholar
• Bienko, M. et al. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat. Methods 10, 122–124 (2013).
  Article CAS Google Scholar