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

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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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).

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