Image-based transcriptomics in thousands of single human cells at single-molecule resolution (original) (raw)

References

  1. Brown, P.O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21, 33–37 (1999).
    Article CAS Google Scholar
  2. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).
    Article CAS Google Scholar
  3. 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
  4. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).
    Article CAS Google Scholar
  5. Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).
    Article CAS Google Scholar
  6. Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2, 666–673 (2012).
    Article CAS Google Scholar
  7. Ramsköld, D. et al. Full-length mRNA-seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30, 777–782 (2012).
    Article Google Scholar
  8. 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
  9. Goetz, J.J. & Trimarchi, J.M. Transcriptome sequencing of single cells with Smart-Seq. Nat. Biotechnol. 30, 763–765 (2012).
    Article CAS Google Scholar
  10. Lau, J.Y. et al. Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet 341, 1501–1504 (1993).
    Article CAS Google Scholar
  11. Kern, D. et al. An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 34, 3196–3202 (1996).
    CAS PubMed PubMed Central Google Scholar
  12. Player, A.N., Shen, L.P., Kenny, D., Antao, V.P. & Kolberg, J.A. Single-copy gene detection using branched DNA (bDNA) in situ hybridization. J. Histochem. Cytochem. 49, 603–612 (2001).
    Article CAS Google Scholar
  13. Kenny, D., Shen, L. & Kolberg, J.A. Detection of viral infection and gene expression in clinical tissue specimens using branched DNA (bDNA) in situ hybridization. J. Histochem. Cytochem. 50, 1219–1227 (2002).
    Article CAS Google Scholar
  14. Ma, X.-J., Wu, X. & Luo, Y. Biomarkers for differentiating melanoma from benign nevus in the skin. US patent application 20120071343 (2012).
  15. Femino, A.M., Fay, F.S., Fogarty, K. & Singer, R.H. Visualization of single RNA transcripts in situ. Science 280, 585–590 (1998).
    Article CAS Google Scholar
  16. Raj, A., van den Bogaard, P., Rifkin, S.A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879 (2008).
    Article CAS Google Scholar
  17. Chartrand, P., Bertrand, E., Singer, R.H. & Long, R.M. Sensitive and high-resolution detection of RNA in situ. Methods Enzymol. 318, 493–506 (2000).
    Article CAS Google Scholar
  18. Bhatt, D.M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279–290 (2012).
    Article CAS Google Scholar
  19. Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
    Article Google Scholar
  20. Raj, A. & Tyagi, S. Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. Methods Enzymol. 472, 365–386 (2010).
    Article CAS Google Scholar
  21. So, L.H. et al. General properties of transcriptional time series in Escherichia coli. Nat. Genet. 43, 554–560 (2011).
    Article CAS Google Scholar
  22. Rämö, P., Sacher, R., Snijder, B., Begemann, B. & Pelkmans, L. CellClassifier: supervised learning of cellular phenotypes. Bioinformatics 25, 3028–3030 (2009).
    Article Google Scholar
  23. Snijder, B. et al. Single-cell analysis of population context advances RNAi screening at multiple levels. Mol. Syst. Biol. 8, 579 (2012).
    Article Google Scholar
  24. Hebenstreit, D. et al. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol. Syst. Biol. 7, 497 (2011).
    Article Google Scholar
  25. Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
    Article Google Scholar
  26. Trcek, T., Larson, D., Moldón, A., Query, C. & Singer, R. Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell 147, 1484–1497 (2011).
    Article CAS Google Scholar
  27. Buganim, Y. et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150, 1209–1222 (2012).
    Article CAS Google Scholar
  28. Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39, D561–D568 (2011).
    Article CAS Google Scholar
  29. Lubeck, E. & Cai, L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat. Methods 9, 743–748 (2012).
    Article CAS Google Scholar
  30. Nguyen, Q.N., Lipshutz, R.J. & Ma, Y. Methods of labeling cells, labeled cells, and uses thereof. US patent application 20120178081 (2012).
  31. Levesque, M.J. & Raj, A. Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nat. Methods 10, 246–248 (2013).
    Article CAS Google Scholar
  32. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    Article Google Scholar
  33. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009).
    Article CAS Google Scholar
  34. 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).
    Article CAS Google Scholar
  35. Martinez, W.L. & Martinez, A.R. Computational Statistics Handbook with MATLAB 2nd edn. (CRC Press, 2008).
  36. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
    Article CAS Google Scholar

Download references