Single-cell mRNA quantification and differential analysis with Census (original) (raw)

• Macosko, E.Z., Basu, A., Satija, R., Nemesh, J. & Shekhar, K. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Klein, A.M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015).
  Article CAS PubMed PubMed Central 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 PubMed PubMed Central Google Scholar
• Grün, D., Kester, L. & van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat. Methods 11, 637–640 (2014).
  Article CAS PubMed Google Scholar
• Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543–1551 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Fu, G.K., Hu, J., Wang, P.-H. & Fodor, S.P.A. Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc. Natl. Acad. Sci. USA 108, 9026–9031 (2011).
  Article PubMed PubMed Central Google Scholar
• Hug, H. & Schuler, R. Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. J. Theor. Biol. 221, 615–624 (2003).
  Article CAS PubMed Google Scholar
• Picelli, S., Faridani, O.R., Björklund, A.K. & Winberg, G. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
  Article CAS PubMed Google Scholar
• Petropoulos, S. et al. Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165, 1012–1026 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Segerstolpe, Å. et al. Single-cell transcriptome profiling of human pancreatic islets in health and type 2 diabetes. Cell Metab. 24, 593–607 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Zeisel, A. et al. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138–1142 (2015).
  Article CAS PubMed 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 PubMed PubMed Central Google Scholar
• Wu, A.R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11, 41–46 (2014).
  Article CAS PubMed Google Scholar
• Treutlein, B. et al. Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature 534, 391–395 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
  Article CAS PubMed Google Scholar
• Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Kharchenko, P.V., Silberstein, L. & Scadden, D.T. Bayesian approach to single-cell differential expression analysis. Nat. Methods 11, 740–742 (2014).
  Article CAS PubMed PubMed Central 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 Cell 6, 468–478 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• 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 PubMed PubMed Central Google Scholar
• Zhou, J.X. & Huang, S. Understanding gene circuits at cell-fate branch points for rational cell reprogramming. Trends Genet. 27, 55–62 (2011).
  Article CAS PubMed Google Scholar
• Moignard, V. et al. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat. Biotechnol. 33, 269–276 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Marco, E. et al. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc. Natl. Acad. Sci. USA 111, E5643–E5650 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371–375 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Hochegger, H., Takeda, S. & Hunt, T. Cyclin-dependent kinases and cell-cycle transitions: does one fit all? Nat. Rev. Mol. Cell Biol. 9, 910–916 (2008).
  Article CAS PubMed Google Scholar
• Desai, T.J., Brownfield, D.G. & Krasnow, M.A. Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature 507, 190–194 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Chi, X., Garnier, G., Hawgood, S. & Colten, H.R. Identification of a novel alternatively spliced mRNA of murine pulmonary surfactant protein B. Am. J. Respir. Cell Mol. Biol. 19, 107–113 (1998).
  Article CAS PubMed Google Scholar
• McCullagh, P. & Nelder, J.A. Generalized Linear Models 2nd edn. (CRC Press, 1989).
• Shu, W. et al. Foxp2 and Foxp1 cooperatively regulate lung and esophagus development. Development 134, 1991–2000 (2007).
  Article CAS PubMed Google Scholar
• Yin, Y. et al. An FGF-WNT gene regulatory network controls lung mesenchyme development. Dev. Biol. 319, 426–436 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Shu, W., Yang, H., Zhang, L., Lu, M.M. & Morrisey, E.E. Characterization of a new subfamily of winged-helix/forkhead (Fox) genes that are expressed in the lung and act as transcriptional repressors. J. Biol. Chem. 276, 27488–27497 (2001).
  Article CAS PubMed Google Scholar
• Wan, H. et al. Kruppel-like factor 5 is required for perinatal lung morphogenesis and function. Development 135, 2563–2572 (2008).
  Article CAS PubMed Google Scholar
• Xu, Y. et al. C/EBPα is required for pulmonary cytoprotection during hyperoxia. Am. J. Physiol. Lung Cell. Mol. Physiol. 297, L286–L298 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Okubo, T. & Hogan, B.L.M. Hyperactive Wnt signaling changes the developmental potential of embryonic lung endoderm. J. Biol. 3, 11 (2004).
  Article PubMed PubMed Central Google Scholar
• Shalek, A.K. et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510, 363–369 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Darnell, J.E. Jr., Kerr, I.M. & Stark, G.R. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 264, 1415–1421 (1994).
  Article CAS PubMed Google Scholar
• Honda, K. et al. IRF-7 is the master regulator of type-I interferon–dependent immune responses. Nature 434, 772–777 (2005).
  Article CAS PubMed Google Scholar
• Gautier, G. et al. A type I interferon autocrine-paracrine loop is involved in Toll-like receptor–induced interleukin-12p70 secretion by dendritic cells. J. Exp. Med. 201, 1435–1446 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Lavin, Y. et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312–1326 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Welch, J.D., Hu, Y. & Prins, J.F. Robust detection of alternative splicing in a population of single cells. Nucleic Acids Res. 44, e73 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Perrin, B.J. & Ervasti, J.M. The actin gene family: function follows isoform. Cytoskeleton 67, 630–634 (2010).
  Article CAS PubMed Google Scholar
• Tondeleir, D., Vandamme, D., Vandekerckhove, J., Ampe, C. & Lambrechts, A. Actin isoform expression patterns during mammalian development and in pathology: insights from mouse models. Cell Motil. Cytoskeleton 66, 798–815 (2009).
  Article CAS PubMed Google Scholar
• Gunning, P., O'Neill, G. & Hardeman, E. Tropomyosin-based regulation of the actin cytoskeleton in time and space. Physiol. Rev. 88, 1–35 (2008).
  Article CAS PubMed 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 PubMed Google Scholar
• Bray, N.L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525–527 (2016).
  Article CAS PubMed Google Scholar
• Kim, J.K., Kolodziejczyk, A.A., Ilicic, T., Teichmann, S.A. & Marioni, J.C. Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat. Commun. 6, 8687 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Amit, I. et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326, 257–263 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Yee, T.W. Vector Generalized Linear and Additive Models (Springer, 2015).
• Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009–1015 (2010).
  Article CAS PubMed PubMed Central 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 PubMed PubMed Central Google Scholar
• Corbel, C., Diabangouaya, P., Gendrel, A.-V., Chow, J.C. & Heard, E. Unusual chromatin status and organization of the inactive X chromosome in murine trophoblast giant cells. Development 140, 861–872 (2013).
  Article CAS PubMed Google Scholar
• Yang, F., Babak, T., Shendure, J. & Disteche, C.M. Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res. 20, 614–622 (2010).
  Article CAS PubMed PubMed Central Google Scholar