Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

Abate, 2009, Beating Poisson encapsulation statistics using close-packed ordering, Lab Chip, 9, 2628, 10.1039/b909386a

Agresti, 2010, Ultrahigh-throughput screening in drop-based microfluidics for directed evolution, Proc. Natl. Acad. Sci. USA, 107, 4004, 10.1073/pnas.0910781107

Amir, 2013, viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia, Nat. Biotechnol., 31, 545, 10.1038/nbt.2594

Baker, 2005, The External RNA Controls Consortium: a progress report, Nat. Methods, 2, 731, 10.1038/nmeth1005-731

Baret, 2009, Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity, Lab Chip, 9, 1850, 10.1039/b902504a

Brennecke, 2013, Accounting for technical noise in single-cell RNA-seq experiments, Nat. Methods, 10, 1093, 10.1038/nmeth.2645

Canham, 2010, Functional heterogeneity of embryonic stem cells revealed through translational amplification of an early endodermal transcript, PLoS Biol., 8, e1000379, 10.1371/journal.pbio.1000379

Chambers, 2007, Nanog safeguards pluripotency and mediates germline development, Nature, 450, 1230, 10.1038/nature06403

Chiang, 2003, Single-cell transcript analysis of pancreas development, Dev. Cell, 4, 383, 10.1016/S1534-5807(03)00035-2

Eastburn, 2013, Ultrahigh-throughput Mammalian single-cell reverse-transcriptase polymerase chain reaction in microfluidic drops, Anal. Chem., 85, 8016, 10.1021/ac402057q

Faast, 2004, Cdk6-cyclin D3 activity in murine ES cells is resistant to inhibition by p16(INK4a), Oncogene, 23, 491, 10.1038/sj.onc.1207133

Fu, 2011, Counting individual DNA molecules by the stochastic attachment of diverse labels, Proc. Natl. Acad. Sci. USA, 108, 9026, 10.1073/pnas.1017621108

Gao, 2013, The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells, Sci Rep., 3, 1588, 10.1038/srep01588

Golan-Mashiach, 2005, Design principle of gene expression used by human stem cells: implication for pluripotency, FASEB J., 19, 147, 10.1096/fj.04-2417fje

Grün, 2014, Validation of noise models for single-cell transcriptomics, Nat. Methods, 11, 637, 10.1038/nmeth.2930

Guo, 2010, Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst, Dev. Cell, 18, 675, 10.1016/j.devcel.2010.02.012

Guo, 2012, Droplet microfluidics for high-throughput biological assays, Lab Chip, 12, 2146, 10.1039/c2lc21147e

Hashimshony, 2012, CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification, Cell Rep., 2, 666, 10.1016/j.celrep.2012.08.003

Hayashi, 2008, Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states, Cell Stem Cell, 3, 391, 10.1016/j.stem.2008.07.027

He, 2009, Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives, J. Biotechnol., 144, 190, 10.1016/j.jbiotec.2009.07.013

Hemberger, 2009, Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington’s canal, Nat. Rev. Mol. Cell Biol., 10, 526, 10.1038/nrm2727

Islam, 2014, Quantitative single-cell RNA-seq with unique molecular identifiers, Nat. Methods, 11, 163, 10.1038/nmeth.2772

Jaitin, 2014, Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types, Science, 343, 776, 10.1126/science.1247651

Kalmar, 2009, Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells, PLoS Biol., 7, e1000149, 10.1371/journal.pbio.1000149

Kégl, 2002, Intrinsic dimension estimation using packing numbers, Paper presented at: Advances in neural information processing systems

Kobayashi, 2009, The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells, Genes Dev., 23, 1870, 10.1101/gad.1823109

Lecault, 2012, Microfluidic single cell analysis: from promise to practice, Curr. Opin. Chem. Biol., 16, 381, 10.1016/j.cbpa.2012.03.022

Li, 2007, Network neighborhood analysis with the multi-node topological overlap measure, Bioinformatics, 23, 222, 10.1093/bioinformatics/btl581

Loewer, 2011, We are all individuals: causes and consequences of non-genetic heterogeneity in mammalian cells, Curr. Opin. Genet. Dev., 21, 753, 10.1016/j.gde.2011.09.010

Losick, 2008, Stochasticity and cell fate, Science, 320, 65, 10.1126/science.1147888

Macosko, 2015, Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets, Cell, 161, 1202, 10.1016/j.cell.2015.05.002

MacArthur, 2012, Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity, Nat. Cell Biol., 14, 1139, 10.1038/ncb2603

Macfarlan, 2012, Embryonic stem cell potency fluctuates with endogenous retrovirus activity, Nature, 487, 57, 10.1038/nature11244

Marčenko, 1967, Dros. Inf. Serv.TRIBUTION OF EIGENVALUES FOR SOME SETS OF RANDOM MATRICES, Mathematics of the USSR-Sbornik, 1, 457, 10.1070/SM1967v001n04ABEH001994

Martinez Arias, 2011, Gene expression heterogeneities in embryonic stem cell populations: origin and function, Curr. Opin. Cell Biol., 23, 650, 10.1016/j.ceb.2011.09.007

Mazutis, 2013, Single-cell analysis and sorting using droplet-based microfluidics, Nat. Protoc., 8, 870, 10.1038/nprot.2013.046

Niakan, 2010, Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal, Genes Dev., 24, 312, 10.1101/gad.1833510

Nishikawa, 1998, Progressive lineage analysis by cell sorting and culture identifies FLK1+VE-cadherin+ cells at a diverging point of endothelial and hemopoietic lineages, Development, 125, 1747, 10.1242/dev.125.9.1747

Ohnishi, 2014, Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages, Nat. Cell Biol., 16, 27, 10.1038/ncb2881

Oka, 1995, Disruption of the mouse RBP-J kappa gene results in early embryonic death, Development, 121, 3291, 10.1242/dev.121.10.3291

Paulsson, 2005, Models of stochastic gene expression, Phys. Life Rev., 2, 157, 10.1016/j.plrev.2005.03.003

Phillips, 1996, Antisense RNA Amplification: A Linear Amplification Method for Analyzing the mRNA Population from Single Living Cells, Methods, 10, 283, 10.1006/meth.1996.0104

Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006

Plerou, 2002, Random matrix approach to cross correlations in financial data, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 65, 066126, 10.1103/PhysRevE.65.066126

Pollen, 2014, Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex, Nat. Biotechnol., 32, 1053, 10.1038/nbt.2967

Qiu, 2011, Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE, Nat. Biotechnol., 29, 886, 10.1038/nbt.1991

Scerbo, 2014, On the origin and evolutionary history of NANOG, PLoS ONE, 9, e85104, 10.1371/journal.pone.0085104

Simons, 2011, Strategies for homeostatic stem cell self-renewal in adult tissues, Cell, 145, 851, 10.1016/j.cell.2011.05.033

Singer, 2014, Dynamic heterogeneity and DNA methylation in embryonic stem cells, Mol. Cell, 55, 319, 10.1016/j.molcel.2014.06.029

Stead, 2002, Pluripotent cell division cycles are driven by ectopic Cdk2, cyclin A/E and E2F activities, Oncogene, 21, 8320, 10.1038/sj.onc.1206015

Streets, 2014, Microfluidic single-cell whole-transcriptome sequencing, Proc. Natl. Acad. Sci. USA, 111, 7048, 10.1073/pnas.1402030111

Swain, 2002, Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc. Natl. Acad. Sci. USA, 99, 12795, 10.1073/pnas.162041399

Teh, 2008, Droplet microfluidics, Lab Chip, 8, 198, 10.1039/b715524g

Torres-Padilla, 2014, Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage, Development, 141, 2173, 10.1242/dev.102624

Toyooka, 2008, Identification and characterization of subpopulations in undifferentiated ES cell culture, Development, 135, 909, 10.1242/dev.017400

Van der Maaten, 2008, Visualizing data using t-SNE, J. Mach. Learn. Res., 9, 85

Wardle, 2004, Refinement of gene expression patterns in the early Xenopus embryo, Development, 131, 4687, 10.1242/dev.01340

White, 2005, Cell cycle control of embryonic stem cells, Stem Cell Rev., 1, 131, 10.1385/SCR:1:2:131

Whitfield, 2002, Identification of genes periodically expressed in the human cell cycle and their expression in tumors, Mol. Biol. Cell, 13, 1977, 10.1091/mbc.02-02-0030

Wu, 2014, Quantitative assessment of single-cell RNA-sequencing methods, Nat. Methods, 11, 41, 10.1038/nmeth.2694

Yamaji, 2013, PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells, Cell Stem Cell, 12, 368, 10.1016/j.stem.2012.12.012

Yan, 2013, Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells, Nat. Struct. Mol. Biol., 20, 1131, 10.1038/nsmb.2660

Yanes, 2010, Metabolic oxidation regulates embryonic stem cell differentiation, Nat. Chem. Biol., 6, 411, 10.1038/nchembio.364

Yang, 2014, Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency, Cell Rep., 7, 1968, 10.1016/j.celrep.2014.05.037