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ABSTRACT High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper
the identification of rare transcripts contained within the RNA repertoire. Herein we present targeted-RNA directional sequencing (TARDIS), a hybridization-based method that allows subsets
of RNAs contained within the transcriptome to be interrogated independently of transcript length, function, the presence or absence of poly-A tracts, or the mechanism of biogenesis. TARDIS
is a modular protocol that is subdivided into four main phases, including the generation of random DNA traps covering the region of interest, purification of input RNA material, DNA
trap–based RNA capture, and finally RNA-sequencing library construction. Importantly, coupling RNA capture to strand-specific RNA sequencing enables robust identification and reconstruction
of novel transcripts, the definition of sense and antisense RNA pairs and, by the concomitant analysis of long and natural small RNA pools, it allows the user to infer potential
precursor-product relations. TARDIS takes ∼10 d to implement. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS
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institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS OPTIMIZED IDENTIFICATION AND CHARACTERIZATION OF SMALL RNAS WITH PANDORA-SEQ
Article 03 April 2025 NAD TAGSEQ FOR TRANSCRIPTOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF NAD+-CAPPED RNAS Article 03 August 2020 GLOBAL IN SITU PROFILING OF RNA-RNA SPATIAL
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actinomycin D. _Nucleic Acids Res._ 35, e128 (2007). Article Google Scholar Download references ACKNOWLEDGEMENTS We thank M. Philipps, S. Vicaire and B. Jost from the IGBMC Microarray and
Sequencing platform (France Génomique consortium—ANR-10-INBS-0009). M.M.P. and V.P. were supported as postdoctoral fellows of the Ligue Nationale Contre le Cancer. This work was supported by
funds from the Alliance Nationale pour les Sciences de la Vie et de la Santé–Institut Thématique Multi-organismes Cancer–Institut National du Cancer (INCa) grant 'Epigenomics of breast
cancer', EpiPCa, the Ligue National Contre le Cancer (to H.G.; Equipe Labellisée), the INCa and the European Community contract LSHC-CT-2005-518417 'EPITRON'. Support from
the Agence Nationale de la Recherche (ANRT-07-PCVI-0031-01, ANR-10-LABX-0030-INRT and ANR-10-IDEX-0002-02) is also acknowledged. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Institut de
Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et
de la Recherche Médicale U964, University of Strasbourg, Illkirch, France Maximiliano M Portal, Valeria Pavet, Cathie Erb & Hinrich Gronemeyer Authors * Maximiliano M Portal View author
publications You can also search for this author inPubMed Google Scholar * Valeria Pavet View author publications You can also search for this author inPubMed Google Scholar * Cathie Erb
View author publications You can also search for this author inPubMed Google Scholar * Hinrich Gronemeyer View author publications You can also search for this author inPubMed Google Scholar
CONTRIBUTIONS M.M.P. conceived and designed the RNA-trap-seq strategy and performed bioinformatics analysis. M.M.P., V.P. and C.E. performed experiments and optimized the final experimental
pipeline. M.M.P., V.P. and H.G. wrote the manuscript. CORRESPONDING AUTHORS Correspondence to Maximiliano M Portal or Hinrich Gronemeyer. ETHICS DECLARATIONS COMPETING INTERESTS A European
patent application, ‘Methods for sequencing and identifying RNAs’ (EP 14 305 822.0) has been filed by M.M.P. and H.G. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE
THIS ARTICLE Portal, M., Pavet, V., Erb, C. _et al._ TARDIS, a targeted RNA directional sequencing method for rare RNA discovery. _Nat Protoc_ 10, 1915–1938 (2015).
https://doi.org/10.1038/nprot.2015.120 Download citation * Published: 29 October 2015 * Issue Date: December 2015 * DOI: https://doi.org/10.1038/nprot.2015.120 SHARE THIS ARTICLE Anyone you
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