Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

[1]  R. Fan,et al.  Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate. , 2017, The Analyst.

[2]  G. Sanguinetti,et al.  scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells , 2018, Nature Communications.

[3]  S. Picelli.  Single-cell RNA-sequencing: The future of genome biology is now , 2017, RNA biology.

[4]  J. C. Love,et al.  Seq-Well: A Portable, Low-Cost Platform for High-Throughput Single-Cell RNA-Seq of Low-Input Samples , 2017 .

[5]  C. Ponting,et al.  Single-Cell Multiomics: Multiple Measurements from Single Cells , 2017, Trends in genetics : TIG.

[6]  Rickard Sandberg,et al.  Single-cell sequencing of the small-RNA transcriptome , 2016, Nature Biotechnology.

[7]  Vikram Agarwal,et al.  Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression , 2016, Molecular cell.

[8]  Peter A. Sims,et al.  An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq , 2016, Scientific Reports.

[9]  Zhigang Xue,et al.  Simultaneous profiling of transcriptome and DNA methylome from a single cell , 2016, Genome Biology.

[10]  W. Reik,et al.  Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity , 2016, Genome Biology.

[11]  Lu Wen,et al.  Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas , 2016, Cell Research.

[12]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[13]  C. Ponting,et al.  Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity , 2015, Nature Methods.

[14]  Allon M. Klein,et al.  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.

[15]  Lisa Fish,et al.  Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement , 2015, Cell.

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

[17]  C. Ponting,et al.  G&T-seq: parallel sequencing of single-cell genomes and transcriptomes , 2015, Nature Methods.

[18]  Debora S. Marks,et al.  MicroRNA control of protein expression noise , 2015, Science.

[19]  Jun Liu,et al.  Characterization of the mammalian miRNA turnover landscape , 2015, Nucleic acids research.

[20]  Z. Ignatova,et al.  Emerging roles of tRNA in adaptive translation, signalling dynamics and disease , 2014, Nature Reviews Genetics.

[21]  Phillip A Sharp,et al.  Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. , 2014, Molecular cell.

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

[23]  Gioele La Manno,et al.  Quantitative single-cell RNA-seq with unique molecular identifiers , 2013, Nature Methods.

[24]  E. Martens-Uzunova,et al.  Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer. , 2013, Cancer letters.

[25]  Mikhail G. Dozmorov,et al.  mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis , 2013, BMC Bioinformatics.

[26]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[27]  Stephen R Quake,et al.  Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos , 2013, Science.

[28]  E. Shapiro,et al.  Single-cell sequencing-based technologies will revolutionize whole-organism science , 2013, Nature Reviews Genetics.

[29]  A. Orth,et al.  Akt-mediated phosphorylation of argonaute 2 downregulates cleavage and upregulates translational repression of MicroRNA targets. , 2013, Molecules and Cells.

[30]  Minping Qian,et al.  Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles , 2013 .

[31]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[32]  Sanghyuk Lee,et al.  miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting , 2012, Nucleic Acids Res..

[33]  T. Hashimshony,et al.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. , 2012, Cell reports.

[34]  R. Sandberg,et al.  Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.

[35]  Michael Wigler,et al.  Genome-wide copy number analysis of single cells , 2012, Nature Protocols.

[36]  M. Tewari,et al.  MicroRNA profiling: approaches and considerations , 2012, Nature Reviews Genetics.

[37]  Grace X. Y. Zheng,et al.  MicroRNAs can generate thresholds in target gene expression , 2011, Nature Genetics.

[38]  S. Linnarsson,et al.  Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. , 2011, Genome research.

[39]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[40]  Paul J. Choi,et al.  Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells , 2010, Science.

[41]  Alok Bhattacharya,et al.  Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood , 2010, BMC Genomics.

[42]  C. Sander,et al.  Target mRNA abundance dilutes microRNA and siRNA activity , 2010, Molecular systems biology.

[43]  Catalin C. Barbacioru,et al.  RNA-Seq analysis to capture the transcriptome landscape of a single cell , 2010, Nature Protocols.

[44]  C. Croce.  Causes and consequences of microRNA dysregulation in cancer , 2009, Nature Reviews Genetics.

[45]  Andrew Tsourkas,et al.  Imaging individual microRNAs in single mammalian cells in situ , 2009, Nucleic acids research.

[46]  Catalin C. Barbacioru,et al.  mRNA-Seq whole-transcriptome analysis of a single cell , 2009, Nature Methods.

[47]  Shangqin Guo,et al.  MicroRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors. , 2008, Developmental cell.

[48]  C. Croce,et al.  MicroRNA signatures in human cancers , 2006, Nature Reviews Cancer.

[49]  Caroline Lee,et al.  220-plex microRNA expression profile of a single cell , 2006, Nature Protocols.

[50]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[51]  C. Croce,et al.  A microRNA expression signature of human solid tumors defines cancer gene targets , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[53]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[54]  Robert H Singer,et al.  Single-Cell Gene Expression Profiling , 2002, Science.

[55]  Rudolf M. Huber,et al.  Combined transcriptome and genome analysis of single micrometastatic cells , 2002, Nature Biotechnology.

[56]  Jun Lu,et al.  microRNA Expression Profiling: Technologies, Insights, and Prospects. , 2015, Advances in experimental medicine and biology.

[57]  A. Ballabio,et al.  MicroRNA target prediction by expression analysis of host genes. , 2009, Genome research.

[58]  S. Cohen,et al.  microRNA functions. , 2007, Annual review of cell and developmental biology.