A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies

[1]  Carmen Birchmeier,et al.  Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function , 2017, Science.

[2]  T. Krude,et al.  Non-coding Y RNAs associate with early replicating euchromatin in concordance with the origin recognition complex , 2017, Journal of Cell Science.

[3]  Thomas R. Cox,et al.  Pre-metastatic niches: organ-specific homes for metastases , 2017, Nature Reviews Cancer.

[4]  Lesley Cheng,et al.  Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery , 2016, RNA biology.

[5]  M. Pfaffl,et al.  Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow , 2016, Nucleic acids research.

[6]  E. Lécuyer,et al.  Comparative transcriptomic analysis of human and Drosophila extracellular vesicles , 2016, Scientific Reports.

[7]  X. Breakefield,et al.  Introduction to Extracellular Vesicles: Biogenesis, RNA Cargo Selection, Content, Release, and Uptake , 2016, Cellular and Molecular Neurobiology.

[8]  F. Kashanchi,et al.  Presence of Viral RNA and Proteins in Exosomes from Cellular Clones Resistant to Rift Valley Fever Virus Infection , 2016, Front. Microbiol..

[9]  Roy Parker,et al.  Circular RNAs Co-Precipitate with Extracellular Vesicles: A Possible Mechanism for circRNA Clearance , 2016, PloS one.

[10]  Tiziana Alberio,et al.  CDKL5 and Shootin1 Interact and Concur in Regulating Neuronal Polarization , 2016, PloS one.

[11]  Y. Wang,et al.  Plasma extracellular RNA profiles in healthy and cancer patients , 2016, Scientific Reports.

[12]  A. Maitra,et al.  Minimally invasive genomic and transcriptomic profiling of visceral cancers by next-generation sequencing of circulating exosomes , 2015, Annals of oncology : official journal of the European Society for Medical Oncology.

[13]  J. Ruidavets,et al.  RNY-derived small RNAs as a signature of coronary artery disease , 2015, BMC Medicine.

[14]  Jiang-xia Zhao,et al.  Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis , 2015, Cell Research.

[15]  Petar Glažar,et al.  Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. , 2015, Molecular cell.

[16]  Petar Glažar,et al.  circBase: a database for circular RNAs , 2014, RNA.

[17]  Wenwei Zhang,et al.  Deep Sequencing of RNA from Three Different Extracellular Vesicle (EV) Subtypes Released from the Human LIM1863 Colon Cancer Cell Line Uncovers Distinct Mirna-Enrichment Signatures , 2014, PloS one.

[18]  C. Théry,et al.  Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. , 2014, Annual review of cell and developmental biology.

[19]  J. Schageman,et al.  Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[20]  D. Martins‐de‐Souza,et al.  The overexpression of a single oncogene (ERBB2/HER2) alters the proteomic landscape of extracellular vesicles , 2014, Proteomics.

[21]  F. van Nieuwerburgh,et al.  Library construction for next-generation sequencing: overviews and challenges. , 2014, BioTechniques.

[22]  Lesley Cheng,et al.  Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood , 2014, Journal of extracellular vesicles.

[23]  David I. K. Martin,et al.  Deep Sequencing of Serum Small RNAs Identifies Patterns of 5′ tRNA Half and YRNA Fragment Expression Associated with Breast Cancer , 2014, Biomarkers in cancer.

[24]  J. Garssen,et al.  Recovery of extracellular vesicles from human breast milk is influenced by sample collection and vesicle isolation procedures , 2014, Journal of extracellular vesicles.

[25]  I. Kurochkin,et al.  Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing , 2013, PeerJ.

[26]  Shanshan Zhu,et al.  Circular intronic long noncoding RNAs. , 2013, Molecular cell.

[27]  K. Lea,et al.  The Complete Exosome Workflow Solution: From Isolation to Characterization of RNA Cargo , 2013, BioMed research international.

[28]  Julia Salzman,et al.  Cell-Type Specific Features of Circular RNA Expression , 2013, PLoS genetics.

[29]  S. Thibodeau,et al.  Characterization of human plasma-derived exosomal RNAs by deep sequencing , 2013, BMC Genomics.

[30]  I. Vorobjev,et al.  Circulating microparticles: square the circle , 2013, BMC Cell Biology.

[31]  Sebastian D. Mackowiak,et al.  Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.

[32]  J. Kjems,et al.  Natural RNA circles function as efficient microRNA sponges , 2013, Nature.

[33]  Michael K. Slevin,et al.  Circular RNAs are abundant, conserved, and associated with ALU repeats. , 2013, RNA.

[34]  J. Lötvall,et al.  EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles , 2013, Journal of extracellular vesicles.

[35]  P. Altevogt,et al.  Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation , 2012, PLoS biology.

[36]  H. Buermans,et al.  Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions , 2012, Nucleic acids research.

[37]  Charles Gawad,et al.  Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types , 2012, PloS one.

[38]  Sebastian D. Mackowiak,et al.  Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2 , 2011, Current protocols in bioinformatics.

[39]  Hamid Cheshmi Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers , 2011 .

[40]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[41]  A. Guha,et al.  Intercellular transfer of the oncogenic receptor EGFRvIII by microvesicles derived from tumour cells , 2008, Nature Cell Biology.

[42]  Luigi Biancone,et al.  Endothelial progenitor cell derived microvesicles activate an angiogenic program in endothelial cells by a horizontal transfer of mRNA. , 2007, Blood.

[43]  J. Lötvall,et al.  Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells , 2007, Nature Cell Biology.

[44]  Aled Clayton,et al.  Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids , 2006, Current protocols in cell biology.

[45]  A. Simpson,et al.  Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. , 1994, BioTechniques.

[46]  H. Dalton The Measurement of the Inequality of Incomes , 1920 .

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