Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

[1]  Sean C. Bendall,et al.  Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis , 2015, Cell.

[2]  Thomas Euler,et al.  Retinal bipolar cells: elementary building blocks of vision , 2014, Nature Reviews Neuroscience.

[3]  Liquan Huang,et al.  Gγ13 colocalizes with gustducin in taste receptor cells and mediates IP3 responses to bitter denatonium , 1999, Nature Neuroscience.

[4]  Srinivas C. Turaga,et al.  Space-time wiring specificity supports direction selectivity in the retina , 2014, Nature.

[5]  Staci A. Sorensen,et al.  Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics , 2016 .

[6]  C. Cepko,et al.  A Core Paired-Type and POU Homeodomain-Containing Transcription Factor Program Drives Retinal Bipolar Cell Gene Expression , 2008, The Journal of Neuroscience.

[7]  C. Barnstable,et al.  The subcellular localization of Otx2 is cell-type specific and developmentally regulated in the mouse retina. , 2000, Brain research. Molecular brain research.

[8]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[9]  H. Wässle,et al.  The Primordial, Blue-Cone Color System of the Mouse Retina , 2005, The Journal of Neuroscience.

[10]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[11]  R. Masland,et al.  The Major Cell Populations of the Mouse Retina , 1998, The Journal of Neuroscience.

[12]  Jean-Loup Guillaume,et al.  Fast unfolding of communities in large networks , 2008, 0803.0476.

[13]  Hans Clevers,et al.  Single-cell messenger RNA sequencing reveals rare intestinal cell types , 2015, Nature.

[14]  Jeff W Lichtman,et al.  Imaging axonal transport of mitochondria in vivo , 2007, Nature Methods.

[15]  J. Sanes,et al.  The types of retinal ganglion cells: current status and implications for neuronal classification. , 2015, Annual review of neuroscience.

[16]  M. Masu,et al.  The mGluR6 5′ Upstream Transgene Sequence Directs a Cell-Specific and Developmentally Regulated Expression in Retinal Rod and ON-Type Cone Bipolar Cells , 1997, The Journal of Neuroscience.

[17]  J. Cloutier,et al.  Kirrel3 is required for the coalescence of vomeronasal sensory neuron axons into glomeruli and for male-male aggression , 2013, Development.

[18]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[19]  David Baltimore,et al.  Germline Transmission and Tissue-Specific Expression of Transgenes Delivered by Lentiviral Vectors , 2002, Science.

[20]  S. Pfaff,et al.  LIM Homeodomain Factors Lhx3 and Lhx4 Assign Subtype Identities for Motor Neurons , 1998, Cell.

[21]  T. Ichinose,et al.  Morphological and physiological analysis of type-5 and other bipolar cells in the Mouse Retina , 2016, Neuroscience.

[22]  J. Sanes,et al.  Synaptotagmin I and II are present in distinct subsets of central synapses , 2007, The Journal of comparative neurology.

[23]  C. Cepko,et al.  Genetic analysis of the homeodomain transcription factor Chx10 in the retina using a novel multifunctional BAC transgenic mouse reporter. , 2004, Developmental biology.

[24]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[25]  W. Taylor,et al.  Localization of the calcium‐binding protein secretagogin in cone bipolar cells of the mammalian retina , 2010, The Journal of comparative neurology.

[26]  Tomomi Ichinose,et al.  Differential signalling and glutamate receptor compositions in the OFF bipolar cell types in the mouse retina , 2016, The Journal of physiology.

[27]  J. N. Kay,et al.  NEUROD6 EXPRESSION DEFINES NOVEL RETINAL AMACRINE CELL SUBTYPES AND REGULATES THEIR FATE , 2011, Nature Neuroscience.

[28]  Nicholas C Spitzer,et al.  Neurotransmitter Switching? No Surprise , 2015, Neuron.

[29]  J. N. Kay,et al.  MEGF10 AND 11 MEDIATE HOMOTYPIC INTERACTIONS REQUIRED FOR MOSAIC SPACING OF RETINAL NEURONS , 2012, Nature.

[30]  W. R. Taylor,et al.  The role of starburst amacrine cells in visual signal processing , 2012, Visual Neuroscience.

[31]  John Aach,et al.  Identification of molecular markers of bipolar cells in the murine retina , 2008, The Journal of comparative neurology.

[32]  I. Amit,et al.  Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types , 2014, Science.

[33]  C. McKerlie,et al.  Control of late off-center cone bipolar cell differentiation and visual signaling by the homeobox gene Vsx1. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  J. Sanes,et al.  Type II Cadherins Guide Assembly of a Direction-Selective Retinal Circuit , 2014, Cell.

[35]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[36]  F. Rieke,et al.  Glutamatergic Monopolar Interneurons Provide a Novel Pathway of Excitation in the Mouse Retina , 2016, Current Biology.

[37]  S. Quake,et al.  A survey of human brain transcriptome diversity at the single cell level , 2015, Proceedings of the National Academy of Sciences.

[38]  Tobias Breuninger,et al.  Chromatic Bipolar Cell Pathways in the Mouse Retina , 2011, The Journal of Neuroscience.

[39]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[40]  D. O'Leary,et al.  Functional classes of cortical projection neurons develop dendritic distinctions by class-specific sculpting of an early common pattern , 1992, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[41]  J. Lichtman,et al.  Development of presynaptic inhibition onto retinal bipolar cell axon terminals is subclass-specific. , 2008, Journal of neurophysiology.

[42]  Thomas Euler,et al.  G protein subunit Gγ13 is coexpressed with Gαo, Gβ3, and Gβ4 in retinal ON bipolar cells , 2002, The Journal of comparative neurology.

[43]  B. Borghuis,et al.  Kainate Receptors Mediate Signaling in Both Transient and Sustained OFF Bipolar Cell Pathways in Mouse Retina , 2014, The Journal of Neuroscience.

[44]  J. Sanes,et al.  Subtype-Specific Regeneration of Retinal Ganglion Cells following Axotomy: Effects of Osteopontin and mTOR Signaling , 2015, Neuron.

[45]  V. Marčenko,et al.  DISTRIBUTION OF EIGENVALUES FOR SOME SETS OF RANDOM MATRICES , 1967 .

[46]  F. Wagner.  GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge , 2015, PloS one.

[47]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[48]  H. Wässle,et al.  Expression analysis of green fluorescent protein in retinal neurons of four transgenic mouse lines , 2009, Neuroscience.

[49]  Michael B. Stadler,et al.  Transcriptional code and disease map for adult retinal cell types , 2012, Nature Neuroscience.

[50]  H. Wässle,et al.  Immunocytochemical description of five bipolar cell types of the mouse retina , 2003, The Journal of comparative neurology.

[51]  H. Niki,et al.  Aberrant responses to acoustic stimuli in mice deficient for neural recognition molecule NB‐2 , 2003, The European journal of neuroscience.

[52]  Santo Fortunato,et al.  Community detection in graphs , 2009, ArXiv.

[53]  Andrew McDavid,et al.  Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments , 2012, Bioinform..

[54]  G. Feng,et al.  Genetic evidence that relative synaptic efficacy biases the outcome of synaptic competition , 2003, Nature.

[55]  L. Gan,et al.  Expression of the LIM‐homeodomain protein Isl1 in the developing and mature mouse retina , 2007, The Journal of comparative neurology.

[56]  George J Augustine,et al.  Imaging synaptic inhibition in transgenic mice expressing the chloride indicator, Clomeleon , 2006, Brain cell biology.

[57]  C. Cepko,et al.  Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors. , 2011, Developmental biology.

[58]  Thomas Euler,et al.  OFF bipolar cells express distinct types of dendritic glutamate receptors in the mouse retina , 2013, Neuroscience.

[59]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[60]  T. Roderick,et al.  Ocular retardation mouse caused by Chx10 homeobox null allele: impaired retinal progenitor proliferation and bipolar cell differentiation , 1996, Nature Genetics.

[61]  S. Linnarsson,et al.  Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing , 2014, Nature Neuroscience.

[62]  Michael B. Stadler,et al.  Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling , 2007, The Journal of comparative neurology.

[63]  New clustering proposals for Twitter based on the Louvain algorithm , 2014 .

[64]  Alex A. Pollen,et al.  Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex , 2014, Nature Biotechnology.

[65]  Stephan Saalfeld,et al.  Globally optimal stitching of tiled 3D microscopic image acquisitions , 2009, Bioinform..

[66]  H. Sebastian Seung,et al.  Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation , 2016, Cell reports.

[67]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[68]  Martin Rosvall,et al.  Maps of random walks on complex networks reveal community structure , 2007, Proceedings of the National Academy of Sciences.

[69]  Srinivas C. Turaga,et al.  Connectomic reconstruction of the inner plexiform layer in the mouse retina , 2013, Nature.

[70]  J. Sanes,et al.  Improved tools for the Brainbow toolbox. , 2013, Nature methods.

[71]  H. Seung,et al.  Neuronal Cell Types and Connectivity: Lessons from the Retina , 2014, Neuron.

[72]  S. Nelson,et al.  A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex , 2011, Neuron.

[73]  H. Wässle,et al.  Cone Contacts, Mosaics, and Territories of Bipolar Cells in the Mouse Retina , 2009, The Journal of Neuroscience.

[74]  Allan R. Jones,et al.  A robust and high-throughput Cre reporting and characterization system for the whole mouse brain , 2009, Nature Neuroscience.

[75]  Masahito Yamagata,et al.  SIDEKICK 2 DIRECTS FORMATION OF A RETINAL CIRCUIT THAT DETECTS DIFFERENTIAL MOTION , 2015, Nature.

[76]  Matt Thomson,et al.  Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. , 2016, Cell systems.