Exponential scaling of single-cell RNA-seq in the past decade (original) (raw)
Gest, H. The discovery of microorganisms by Robert Hooke and Antoni Van Leeuwenhoek, fellows of the Royal Society. Notes Rec. R. Soc. Lond.58, 187–201 (2004). Article Google Scholar
Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet.17, 744–757 (2016). ArticleCAS Google Scholar
Poulin, J.-F., Tasic, B., Hjerling-Leffler, J., Trimarchi, J.M. & Awatramani, R. Disentangling neural cell diversity using single-cell transcriptomics. Nat. Neurosci.19, 1131–1141 (2016). Article Google Scholar
Mosmann, T.R., Cherwinski, H., Bond, M.W., Giedlin, M.A. & Coffman, R.L. Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. J. Immunol.136, 2348–2357 (1986). CAS Google Scholar
Orkin, S.H. Diversification of haematopoietic stem cells to specific lineages. Nat. Rev. Genet.1, 57–64 (2000). ArticleCAS Google Scholar
Zhu, J. Transcriptional regulation of Th2 cell differentiation. Immunol. Cell Biol.88, 244–249 (2010). ArticleCAS Google Scholar
Ivanov, I.I., Zhou, L. & Littman, D.R. Transcriptional regulation of Th17 cell differentiation. Semin. Immunol.19, 409–417 (2007). ArticleCAS Google Scholar
Trapnell, C. Defining cell types and states with single-cell genomics. Genome Res.25, 1491–1498 (2015). ArticleCAS Google Scholar
Kolodziejczyk, A.A., Kim, J.K., Svensson, V., Marioni, J.C. & Teichmann, S.A. The technology and biology of single-cell RNA sequencing. Mol. Cell58, 610–620 (2015). 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
Lambolez, B., Audinat, E., Bochet, P., Crépel, F. & Rossier, J. AMPA receptor subunits expressed by single Purkinje cells. Neuron9, 247–258 (1992). ArticleCAS Google Scholar
Peixoto, A., Monteiro, M., Rocha, B. & Veiga-Fernandes, H. Quantification of multiple gene expression in individual cells. Genome Res.14, 1938–1947 (2004). ArticleCAS Google Scholar
Sheng, H.Z., Lin, P.X. & Nelson, P.G. Analysis of multiple heterogeneous mRNAs in single cells. Anal. Biochem.222, 123–130 (1994). ArticleCAS Google Scholar
Tietjen, I. et al. Single-cell transcriptional analysis of neuronal progenitors. Neuron38, 161–175 (2003). ArticleCAS 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). ArticleCAS Google Scholar
Esumi, S. et al. Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors. Neurosci. Res.60, 439–451 (2008). ArticleCAS Google Scholar
Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods6, 377–382 (2009). ArticleCAS Google Scholar
Tang, F. et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell6, 468–478 (2010). ArticleCAS Google Scholar
Tang, F. et al. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One6, e21208 (2011). ArticleCAS Google Scholar
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
Brouilette, S. et al. A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase. Dev. Dyn.241, 1584–1590 (2012). ArticleCAS Google Scholar
Guo, G. et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev. Cell18, 675–685 (2010). ArticleCAS Google Scholar
Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res.21, 1160–1167 (2011). ArticleCAS Google Scholar
Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science347, 1138–1142 (2015). ArticleCAS 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). ArticleCAS Google Scholar
Svensson, V. et al. Power analysis of single-cell RNA-sequencing experiments. Nat. Methods14, 381–387 (2017). ArticleCAS Google Scholar
Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods10, 1096–1098 (2013). ArticleCAS Google Scholar
Boon, W.C. et al. Increasing cDNA yields from single-cell quantities of mRNA in standard laboratory reverse transcriptase reactions using acoustic microstreaming. J. Vis. Exp.3144, e3144 (2011). Google Scholar
Klein, C.A. et al. Combined transcriptome and genome analysis of single micrometastatic cells. Nat. Biotechnol.20, 387–392 (2002). ArticleCAS Google Scholar
Zhu, Y.Y., Machleder, E.M., Chenchik, A., Li, R. & Siebert, P.D. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques30, 892–897 (2001). ArticleCAS Google Scholar
Baugh, L.R., Hill, A.A., Brown, E.L. & Hunter, C.P. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res.29, E29 (2001). ArticleCAS Google Scholar
Jaitin, D.A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science343, 776–779 (2014). ArticleCAS Google Scholar
Klein, A.M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell161, 1187–1201 (2015). ArticleCAS Google Scholar
Vickovic, S. et al. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat. Commun.7, 13182 (2016). ArticleCAS Google Scholar
Muraro, M.J. et al. A single-cell transcriptome atlas of the human pancreas. Cell Syst.3, 385–394 (2016). ArticleCAS Google Scholar
Lönnberg, T. et al. Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria. Sci. Immunol.2, eaal2192 (2017). Article Google Scholar
Shalek, A.K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature498, 236–240 (2013). ArticleCAS Google Scholar
Mazutis, L. et al. Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protoc.8, 870–891 (2013). ArticleCAS Google Scholar
Macosko, E.Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell161, 1202–1214 (2015). ArticleCAS Google Scholar
Gierahn, T.M. et al. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods14, 395–398 (2017). ArticleCAS Google Scholar
Fan, H.C., Fu, G.K. & Fodor, S.P.A. Combinatorial labeling of single cells for gene expression cytometry. Science347, 1258367 (2015). Article Google Scholar
Bose, S. et al. Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol.16, 120 (2015). Article Google Scholar
Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep.2, 666–673 (2012). ArticleCAS Google Scholar
Zheng, G.X.Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun.8, 14049 (2017). ArticleCAS Google Scholar
Costea, P.I., Lundeberg, J. & Akan, P. TagGD: fast and accurate software for DNA Tag generation and demultiplexing. PLoS One8, e57521 (2013). ArticleCAS Google Scholar
Cusanovich, D.A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science348, 910–914 (2015). ArticleCAS Google Scholar
Vitak, S.A. et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat. Methods14, 302–308 (2017). ArticleCAS Google Scholar
Ramani, V. et al. Massively multiplex single-cell Hi-C. Nat. Methods14, 263–266 (2017). ArticleCAS Google Scholar
Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods14, 955–958 (2017). ArticleCAS Google Scholar
Lake, B.B. et al. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science352, 1586–1590 (2016). ArticleCAS Google Scholar
Lake, B.B. et al. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci. Rep.7, 6031 (2017). Article Google Scholar
Lee, J.H. Quantitative approaches for investigating the spatial context of gene expression. Wiley Interdiscip. Rev. Syst. Biol. Med.9, e1369 (2017). Article Google Scholar
Ståhl, P.L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science353, 78–82 (2016). Article Google Scholar
Moffitt, J.R. et al. High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. Proc. Natl. Acad. Sci. USA113, 14456–14461 (2016). ArticleCAS Google Scholar
Moffitt, J.R. et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl. Acad. Sci. USA113, 11046–11051 (2016). ArticleCAS Google Scholar
Shah, S., Lubeck, E., Zhou, W. & Cai, L. In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron92, 342–357 (2016). ArticleCAS Google Scholar
Lee, J.H. et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat. Protoc.10, 442–458 (2015). ArticleCAS Google Scholar
Lee, J.H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science343, 1360–1363 (2014). ArticleCAS Google Scholar