Searching journal content for articles similar to Reicher et al. 30 (12): 1846.

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  1. Research: Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
    • Dorothee Pflueger,
    • Stéphane Terry,
    • Andrea Sboner,
    • Lukas Habegger,
    • Raquel Esgueva,
    • Pei-Chun Lin,
    • Maria A. Svensson,
    • Naoki Kitabayashi,
    • Benjamin J. Moss,
    • Theresa Y. MacDonald,
    • Xuhong Cao,
    • Terrence Barrette,
    • Ashutosh K. Tewari,
    • Mark S. Chee,
    • Arul M. Chinnaiyan,
    • David S. Rickman,
    • Francesca Demichelis,
    • Mark B. Gerstein,
    • and Mark A. Rubin
    Genome Res. January 2011 21: 56-67; Published in Advance October 29, 2010, doi:10.1101/gr.110684.110
    ...the initial list of candidate fusion transcripts of ;96% on average, thus enriching for potentially real fusion transcripts (Supplemental Table S2). Also, similar to Table 1. Summary statistics of data generation with next-generation RNA sequencing Sample Tissue type ETS fusion No. of lanes Read length No...
  2. Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Melissa J. Fullwood,
    • Chia-Lin Wei,
    • Edison T. Liu,
    • and Yijun Ruan
    Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
    ...Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses Melissa J. Fullwood 1 , 2 , Chia-Lin Wei 1 , Edison T. Liu 1 , 3 and Yijun Ruan 1 , 4 , 5 1 Genome Institute of Singapore, Agency...
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  3. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...techniques have been developed that monitor transcription as it occurs. Pioneering work introduced methods such as global run-on sequencing (GRO-seq) (Core and Lis 2008) and precision nuclear run-on sequencing (PRO-seq) (Kwak et al. 2013), which measure the location and activity of engaged RNA polymerase II...
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  4. PERSPECTIVE: Hunting with Traps: Genome-Wide Strategies for Gene Discovery and Functional Analysis
    • Kyle Durick,
    • John Mendlein,
    • and Kleanthis G. Xanthopoulos
    Genome Res. November 1, 1999 9: 1019-1025; doi:10.1101/gr.9.11.1019
    ...cells in which the tagging element has inserted into an actively transcribed gene. A new and highly sensitive reporter system has recently been described and is well suited for gene tagging. A nontoxic fluorescent substrate of β-lactamase, CCF2-AM, enables real-time and sensitive monitoring...
  5. REVIEW: Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends
    • Deirdre Meldrum
    Genome Res. September 1, 2000 10: 1288-1303; doi:10.1101/gr.157400
    ...operations. The LI-COR, Inc. (Lincoln, NE) ( http://www.licor.com ) Model 4200 (IR2) automated DNA sequencer, launched in 1997, is a two-dye near-infrared DNA analysis system. It can detect the products of two different sequencing reactions in parallel enabling pooling reactions and simultaneous...
  6. Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
    • Rosario Avolio,
    • Ilenia Agliarulo,
    • Daniela Criscuolo,
    • Daniela Sarnataro,
    • Margherita Auriemma,
    • Sabrina De Lella,
    • Sara Pennacchio,
    • Giovanni Calice,
    • Martin Y. Ng,
    • Carlotta Giorgi,
    • Paolo Pinton,
    • Barry S. Cooperman,
    • Matteo Landriscina,
    • Franca Esposito,
    • and Danilo Swann Matassa
    Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
    ...and increased upon shRNA-mediated silencing (Supplemental Fig. S2A). TRAP1 silencing with two different siRNA sequences in both HeLa and HT29 colorectal carcinoma cells yielded analogous results in fluorescent noncanonical amino acid tagging (FUNCAT) assays (Supplemental Fig. S2B).View larger version...
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  7. Resource: Functional annotation of human long noncoding RNAs via molecular phenotyping
    • Jordan A. Ramilowski,
    • Chi Wai Yip,
    • Saumya Agrawal,
    • Jen-Chien Chang,
    • Yari Ciani,
    • Ivan V. Kulakovskiy,
    • Mickaël Mendez,
    • Jasmine Li Ching Ooi,
    • John F. Ouyang,
    • Nick Parkinson,
    • Andreas Petri,
    • Leonie Roos,
    • Jessica Severin,
    • Kayoko Yasuzawa,
    • Imad Abugessaisa,
    • Altuna Akalin,
    • Ivan V. Antonov,
    • Erik Arner,
    • Alessandro Bonetti,
    • Hidemasa Bono,
    • Beatrice Borsari,
    • Frank Brombacher,
    • Christopher J.F. Cameron,
    • Carlo Vittorio Cannistraci,
    • Ryan Cardenas,
    • Melissa Cardon,
    • Howard Chang,
    • Josée Dostie,
    • Luca Ducoli,
    • Alexander Favorov,
    • Alexandre Fort,
    • Diego Garrido,
    • Noa Gil,
    • Juliette Gimenez,
    • Reto Guler,
    • Lusy Handoko,
    • Jayson Harshbarger,
    • Akira Hasegawa,
    • Yuki Hasegawa,
    • Kosuke Hashimoto,
    • Norihito Hayatsu,
    • Peter Heutink,
    • Tetsuro Hirose,
    • Eddie L. Imada,
    • Masayoshi Itoh,
    • Bogumil Kaczkowski,
    • Aditi Kanhere,
    • Emily Kawabata,
    • Hideya Kawaji,
    • Tsugumi Kawashima,
    • S. Thomas Kelly,
    • Miki Kojima,
    • Naoto Kondo,
    • Haruhiko Koseki,
    • Tsukasa Kouno,
    • Anton Kratz,
    • Mariola Kurowska-Stolarska,
    • Andrew Tae Jun Kwon,
    • Jeffrey Leek,
    • Andreas Lennartsson,
    • Marina Lizio,
    • Fernando López-Redondo,
    • Joachim Luginbühl,
    • Shiori Maeda,
    • Vsevolod J. Makeev,
    • Luigi Marchionni,
    • Yulia A. Medvedeva,
    • Aki Minoda,
    • Ferenc Müller,
    • Manuel Muñoz-Aguirre,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Kazuhiro R. Nitta,
    • Shuhei Noguchi,
    • Yukihiko Noro,
    • Ramil Nurtdinov,
    • Yasushi Okazaki,
    • Valerio Orlando,
    • Denis Paquette,
    • Callum J.C. Parr,
    • Owen J.L. Rackham,
    • Patrizia Rizzu,
    • Diego Fernando Sánchez Martinez,
    • Albin Sandelin,
    • Pillay Sanjana,
    • Colin A.M. Semple,
    • Youtaro Shibayama,
    • Divya M. Sivaraman,
    • Takahiro Suzuki,
    • Suzannah C. Szumowski,
    • Michihira Tagami,
    • Martin S. Taylor,
    • Chikashi Terao,
    • Malte Thodberg,
    • Supat Thongjuea,
    • Vidisha Tripathi,
    • Igor Ulitsky,
    • Roberto Verardo,
    • Ilya E. Vorontsov,
    • Chinatsu Yamamoto,
    • Robert S. Young,
    • J. Kenneth Baillie,
    • Alistair R.R. Forrest,
    • Roderic Guigó,
    • Michael M. Hoffman,
    • Chung Chau Hon,
    • Takeya Kasukawa,
    • Sakari Kauppinen,
    • Juha Kere,
    • Boris Lenhard,
    • Claudio Schneider,
    • Harukazu Suzuki,
    • Ken Yagi,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • and Piero Carninci
    Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
    ...oligonucleotide (ASO) technology (Roux et al. 2017). We then quantified the effect of each knockdown on cell growth and morphology using real-time imaging, followed by Cap Analysis Gene Expression (CAGE) (Murata et al. 2014) deep sequencing to reveal molecular pathways associated with each lncRNA. In contrast...
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  8. LETTER: Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
    • W. Troy Loging,
    • Anita Lal,
    • I-Mei Siu,
    • Tania L. Loney,
    • Carol J. Wikstrand,
    • Marco A. Marra,
    • Christa Prange,
    • Darell D. Bigner,
    • Robert L. Strausberg,
    • and Gregory J. Riggins
    Genome Res. September 1, 2000 10: 1393-1402; doi:10.1101/gr.138000
    ...et al. 1999 ). F-PEC data could augment tissue microarray analysis, in particular when an antibody or in situ hybridization assay is not readily available for a particular gene. Regardless of the follow-up approach, there is a real need to be able to rapidly assess well-documented samples...
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