Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue (original) (raw)
Kaern, M., Elston, T.C., Blake, W.J. & Collins, J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet.6, 451–464 (2005). ArticleCAS Google Scholar
Raj, A. & van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell135, 216–226 (2008). ArticleCAS Google Scholar
Eldar, A. & Elowitz, M.B. Functional roles for noise in genetic circuits. Nature467, 167–173 (2010). ArticleCAS Google Scholar
Elowitz, M.B., Levine, A.J., Siggia, E.D. & Swain, P.S. Stochastic gene expression in a single cell. Science297, 1183–1186 (2002). ArticleCAS Google Scholar
Flatz, L. et al. Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines. Proc. Natl. Acad. Sci. USA108, 5724–5729 (2011). ArticleCAS Google Scholar
Taniguchi, Y. et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science329, 533–538 (2010). ArticleCAS Google Scholar
Pedraza, J.M. & van Oudenaarden, A. Noise propagation in gene networks. Science307, 1965–1969 (2005). ArticleCAS Google Scholar
Cahoy, J.D. et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci.28, 264–278 (2008). ArticleCAS Google Scholar
Lovatt, D. et al. The transcriptome and metabolic gene signature of protoplasmic astrocytes in the adult murine cortex. J. Neurosci.27, 12255–12266 (2007). ArticleCAS Google Scholar
Sugino, K. et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat. Neurosci.9, 99–107 (2006). ArticleCAS Google Scholar
Eberwine, J. et al. Quantitative biology of single neurons. J. R. Soc. Interface9, 3165–3183 (2012). ArticleCAS Google Scholar
Espina, V. et al. Laser-capture microdissection. Nat. Protoc.1, 586–603 (2006). ArticleCAS Google Scholar
Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods6, 377–382 (2009). ArticleCAS Google Scholar
Okaty, B.W., Sugino, K. & Nelson, S.B. A quantitative comparison of cell-type-specific microarray gene expression profiling methods in the mouse brain. PLoS ONE6, e16493 (2011). ArticleCAS Google Scholar
Joliot, A. & Prochiantz, A. Transduction peptides: from technology to physiology. Nat. Cell Biol.6, 189–196 (2004). ArticleCAS Google Scholar
Kumar, P. et al. Transvascular delivery of small interfering RNA to the central nervous system. Nature448, 39–43 (2007). ArticleCAS Google Scholar
Zeng, F. et al. A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells. Nat. Protoc.1, 920–927 (2006). ArticleCAS Google Scholar
Zielinski, J. et al. In vivo identification of ribonucleoprotein-RNA interactions. Proc. Natl. Acad. Sci. USA103, 1557–1562 (2006). ArticleCAS Google Scholar
Adams, S.R. & Tsien, R.Y. Controlling cell chemistry with caged compounds. Annu. Rev. Physiol.55, 755–784 (1993). ArticleCAS Google Scholar
Tang, X. & Dmochowski, I.J. Synthesis of light-activated antisense oligodeoxynucleotide. Nat. Protoc.1, 3041–3048 (2006). ArticleCAS Google Scholar
Dmochowski, I.J. & Tang, X. Taking control of gene expression with light-activated oligonucleotides. Biotechniques43, 161–165 (2007). ArticleCAS Google Scholar
Madani, F., Lindberg, S., Langel, U., Futaki, S. & Graslund, A. Mechanisms of cellular uptake of cell-penetrating peptides. J. Biophys.2011, 414729 (2011). Article Google Scholar
Svensen, N., Walton, J.G. & Bradley, M. Peptides for cell-selective drug delivery. Trends Pharmacol. Sci.33, 186–192 (2012). ArticleCAS Google Scholar
Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods5, 507–516 (2008). ArticleCAS Google Scholar
Eberwine, J. et al. Analysis of gene expression in single live neurons. Proc. Natl. Acad. Sci. USA89, 3010–3014 (1992). ArticleCAS Google Scholar
Morris, J., Singh, J.M. & Eberwine, J.H. Transcriptome analysis of single cells. J. Vis. Exp.2011, 2634 (2011). Google Scholar
Ramskold, 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
Griffith, M. et al. Alternative expression analysis by RNA sequencing. Nat. Methods7, 843–847 (2010). ArticleCAS Google Scholar
Zheng, W., Chung, L.M. & Zhao, H. Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics12, 290 (2011). ArticleCAS Google Scholar
Adiconis, X. et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods10, 623–629 (2013). ArticleCAS Google Scholar
Gertz, J. et al. Transposase mediated construction of RNA-seq libraries. Genome Res.22, 134–141 (2012). ArticleCAS Google Scholar
Ellis-Davies, G.C. Caged compounds: photorelease technology for control of cellular chemistry and physiology. Nat. Methods4, 619–628 (2007). ArticleCAS Google Scholar
Zhang, S.C. Defining glial cells during CNS development. Nat. Rev. Neurosci.2, 840–843 (2001). ArticleCAS Google Scholar
Pribyl, T.M. et al. Expression of the myelin basic protein gene locus in neurons and oligodendrocytes in the human fetal central nervous system. J. Comp. Neurol.374, 342–353 (1996). ArticleCAS Google Scholar
Landry, C.F. et al. Myelin basic protein gene expression in neurons: developmental and regional changes in protein targeting within neuronal nuclei, cell bodies, and processes. The J. Neurosci.16, 2452–2462 (1996). ArticleCAS Google Scholar
Vives, V., Alonso, G., Solal, A.C., Joubert, D. & Legraverend, C. Visualization of S100B-positive neurons and glia in the central nervous system of EGFP transgenic mice. J. Comp. Neurol.457, 404–419 (2003). ArticleCAS Google Scholar
West, A.E., Griffith, E.C. & Greenberg, M.E. Regulation of transcription factors by neuronal activity. Nat. Rev. Neurosci.3, 921–931 (2002). ArticleCAS Google Scholar
Turner, J.J. et al. Cell-penetrating peptide conjugates of peptide nucleic acids (PNA) as inhibitors of HIV-1 Tat-dependent trans-activation in cells. Nucleic Acids Res.33, 6837–6849 (2005). ArticleCAS Google Scholar
Richards, J.L., Tang, X., Turetsky, A. & Dmochowski, I.J. RNA bandages for photoregulating in vitro protein synthesis. Bioorg. Med. Chem. Lett.18, 6255–6258 (2008). ArticleCAS Google Scholar
Cummings, D.D., Wilcox, K.S. & Dichter, M.A. Calcium-dependent paired-pulse facilitation of miniature EPSC frequency accompanies depression of EPSCs at hippocampal synapses in culture. J. Neurosci.16, 5312–5323 (1996). ArticleCAS Google Scholar
Grant, G.R. et al. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics27, 2518–2528 (2011). ArticleCAS Google Scholar
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol.11, R106 (2010). ArticleCAS Google Scholar