C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
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Jay W. Shin | C. Hon | Piero Carninci | Harukazu Suzuki | T. Lassmann | T. Kasukawa | M. Furuno | T. Arakawa | C. Plessy | J. Severin | E. Arner | N. Ramalingam | Jay A. West | T. Kouno | A. T. Kwon | I. Abugessaisa | Mickaël Mendez | A. Hasegawa | S. Takizawa | Efthymios Motakis | Jonathan Moody | Youtaro Shibayama | Yi Huang | Michael Böttcher | J. Luginbühl | S. Kato | Tsukasa Kouno
[1] Efthymios Motakis,et al. CONFESS: Fluorescence-based single-cell ordering in R , 2018, bioRxiv.
[2] I. Nikaido,et al. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs , 2018, Nature Communications.
[3] I. Nikaido,et al. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs , 2018, Nature Communications.
[4] Benoît Ballester,et al. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments , 2017, Nucleic Acids Res..
[5] Sachi Kato,et al. SCPortalen: human and mouse single-cell centric database , 2017, Nucleic Acids Res..
[6] S. Picelli. Single-cell RNA-sequencing: The future of genome biology is now , 2017, RNA biology.
[7] Jordan A. Ramilowski,et al. An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.
[8] Jay W. Shin,et al. Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells , 2016, bioRxiv.
[9] Matthew R. Krause,et al. Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription , 2016, Nucleic acids research.
[10] A. Regev,et al. Revealing the vectors of cellular identity with single-cell genomics , 2016, Nature Biotechnology.
[11] Valentine Svensson,et al. Power Analysis of Single Cell RNA-Sequencing Experiments , 2016, Nature Methods.
[12] M. Schaub,et al. SC3 - consensus clustering of single-cell RNA-Seq data , 2016, Nature Methods.
[13] Davis J. McCarthy,et al. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.
[14] John C Marioni,et al. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.
[15] David A. Knowles,et al. Batch effects and the effective design of single-cell gene expression studies , 2016, Scientific Reports.
[16] Hongkai Ji,et al. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis , 2016, Nucleic acids research.
[17] J. Marioni,et al. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts , 2016, Genome Biology.
[18] Fidel Ramírez,et al. deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..
[19] C. Plessy,et al. Targeted reduction of highly abundant transcripts using pseudo-random primers. , 2016, BioTechniques.
[20] M. Rosenfeld,et al. Enhancers as non-coding RNA transcription units: recent insights and future perspectives , 2016, Nature Reviews Genetics.
[21] David J. Arenillas,et al. CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs , 2016, bioRxiv.
[22] J. Mesirov,et al. The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .
[23] David J. Arenillas,et al. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles , 2015, Nucleic Acids Res..
[24] Cole Trapnell,et al. Defining cell types and states with single-cell genomics , 2015, Genome research.
[25] Sarah A Teichmann,et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. , 2015, Methods.
[26] Ning Leng,et al. Oscope identifies oscillatory genes in unsynchronized single cell RNA-seq experiments , 2015, Nature Methods.
[27] X. Zhuang,et al. Spatially resolved, highly multiplexed RNA profiling in single cells , 2015, Science.
[28] S. Itzkovitz,et al. Bursty gene expression in the intact mammalian liver. , 2015, Molecular cell.
[29] Thomas J. Ha,et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.
[30] Michael Q. Zhang,et al. Integrative analysis of 111 reference human epigenomes , 2015, Nature.
[31] Timo Lassmann,et al. TagDust2: a generic method to extract reads from sequencing data , 2015, BMC Bioinformatics.
[32] M. Daly,et al. Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants , 2014, Nature.
[33] David P. Kreil,et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures , 2014, Nature Communications.
[34] C. Glass,et al. Enhancer RNAs and regulated transcriptional programs. , 2014, Trends in biochemical sciences.
[35] Cesare Furlanello,et al. A promoter-level mammalian expression atlas , 2015 .
[36] T. Meehan,et al. An atlas of active enhancers across human cell types and tissues , 2014, Nature.
[37] Yoshihide Hayashizaki,et al. Interactive visualization and analysis of large-scale sequencing datasets using ZENBU , 2014, Nature Biotechnology.
[38] P. Spanheimer,et al. TFAP2C Governs the Luminal Epithelial Phenotype in Mammary Development and Carcinogenesis , 2014, Oncogene.
[39] Gioele La Manno,et al. Quantitative single-cell RNA-seq with unique molecular identifiers , 2013, Nature Methods.
[40] Yibin Kang,et al. Transcriptional control of cancer metastasis. , 2013, Trends in cell biology.
[41] N. Neff,et al. Quantitative assessment of single-cell RNA-sequencing methods , 2013, Nature Methods.
[42] L. Grøntved,et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. , 2013, Molecular cell.
[43] James A. DeCaprio,et al. The DREAM complex: master coordinator of cell cycle-dependent gene expression , 2013, Nature Reviews Cancer.
[44] Piero Carninci,et al. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching , 2012, Nucleic acids research.
[45] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[46] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[47] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[48] C. Heldin,et al. Regulation of EMT by TGFβ in cancer , 2012, FEBS letters.
[49] G. Smyth,et al. Camera: a competitive gene set test accounting for inter-gene correlation , 2012, Nucleic acids research.
[50] H. Hurst,et al. Histone Demethylase KDM5B Collaborates with TFAP2C and Myc To Repress the Cell Cycle Inhibitor p21cip (CDKN1A) , 2012, Molecular and Cellular Biology.
[51] David Schneider,et al. Dynamics of TGF-β induced epithelial-to-mesenchymal transition monitored by electric cell-substrate impedance sensing. , 2011, Biochimica et biophysica acta.
[52] Nacho Molina,et al. Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics , 2011, Science.
[53] Carsten O. Daub,et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan , 2010, Nature Methods.
[54] Kohei Miyazono,et al. TGFβ signalling: a complex web in cancer progression , 2010, Nature Reviews Cancer.
[55] Matthew D. Young,et al. Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.
[56] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[57] Christopher Williams,et al. AP‐2γ promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene , 2009, The EMBO journal.
[58] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[59] S. Friedman,et al. TGF-beta regulates the expression of transcription factor KLF6 and its splice variants and promotes co-operative transactivation of common target genes through a Smad3-Sp1-KLF6 interaction. , 2009, Biochemical Journal.
[60] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[61] H. Baker,et al. ALDH isozymes downregulation affects cell growth, cell motility and gene expression in lung cancer cells , 2008, Molecular Cancer.
[62] Y. Qiu,et al. Gfi-1 represses CDKN2B encoding p15INK4B through interaction with Miz-1 , 2008, Proceedings of the National Academy of Sciences.
[63] Scott A. Rifkin,et al. Imaging individual mRNA molecules using multiple singly labeled probes , 2008, Nature Methods.
[64] J. Massagué,et al. TGFβ in Cancer , 2008, Cell.
[65] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[66] J. Kawai,et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[67] Jin Hong Liu,et al. Functional association of TGF-β receptor II with cyclin B , 1999, Oncogene.
[68] F S Fay,et al. Visualization of single RNA transcripts in situ. , 1998, Science.
[69] A. Akeson,et al. A fluorometric assay for the quantitation of cell adherence to endothelial cells. , 1993, Journal of immunological methods.
[70] M. Mhlanga,et al. Visualization of Enhancer-Derived Noncoding RNA. , 2017, Methods in molecular biology.
[71] M. Harbers,et al. NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes. , 2017, Methods in molecular biology.
[72] J. Mesirov,et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.
[73] Piero Carninci,et al. Detecting expressed genes using CAGE. , 2014, Methods in molecular biology.