Searching journal content for articles similar to Stollberg et al. 10 (8): 1241.

Displaying results 1-10 of 106
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  1. Method: Gene expression profiling of human breast tissue samples using SAGE-Seq
    • Zhenhua Jeremy Wu,
    • Clifford A. Meyer,
    • Sibgat Choudhury,
    • Michail Shipitsin,
    • Reo Maruyama,
    • Marina Bessarabova,
    • Tatiana Nikolskaya,
    • Saraswati Sukumar,
    • Armin Schwartzman,
    • Jun S. Liu,
    • Kornelia Polyak,
    • and X. Shirley Liu
    Genome Res. December 2010 20: 1730-1739; Published in Advance November 2, 2010, doi:10.1101/gr.108217.110
    ...). Appropriate global diversitymeasurementswithin and across data sets are evaluated and used to cluster the libraries. We propose amapping strategy to align SAGE-Seq tags to the .We utilize themapping information tominimize sequencing errors andobtain accurate quantification of sense and antisense transcripts...
  2. Methods: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines
    • Jaswinder Khattra,
    • Allen D. Delaney,
    • Yongjun Zhao,
    • Asim Siddiqui,
    • Jennifer Asano,
    • Helen McDonald,
    • Pawan Pandoh,
    • Noreen Dhalla,
    • Anna-liisa Prabhu,
    • Kevin Ma,
    • Stephanie Lee,
    • Adrian Ally,
    • Angela Tam,
    • Danne Sa,
    • Sean Rogers,
    • David Charest,
    • Jeff Stott,
    • Scott Zuyderduyn,
    • Richard Varhol,
    • Connie Eaves,
    • Steven Jones,
    • Robert Holt,
    • Martin Hirst,
    • Pamela A. Hoodless,
    • and Marco A. Marra
    Genome Res. January 2007 17: 108-116; Published in Advance November 29, 2006, doi:10.1101/gr.5488207
    ...the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling. Footnotes ↵ 4...
  3. Resource: A quantitative atlas of polyadenylation in five mammals
    • Adnan Derti,
    • Philip Garrett-Engele,
    • Kenzie D. MacIsaac,
    • Richard C. Stevens,
    • Shreedharan Sriram,
    • Ronghua Chen,
    • Carol A. Rohl,
    • Jason M. Johnson,
    • and Tomas Babak
    Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
    ...A quantitative atlas of polyadenylation in five mammals Adnan Derti 1 , 4 , Philip Garrett-Engele 2 , Kenzie D. MacIsaac 3 , Richard C. Stevens 2 , Shreedharan Sriram 1 , Ronghua Chen 1 , Carol A. Rohl 1 , Jason M...
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  4. LETTER: Quantitative evidence for conserved longevity pathways between divergent eukaryotic species
    • Erica D. Smith,
    • Mitsuhiro Tsuchiya,
    • Lindsay A. Fox,
    • Nick Dang,
    • Di Hu,
    • Emily O. Kerr,
    • Elijah D. Johnston,
    • Bie N. Tchao,
    • Diana N. Pak,
    • K. Linnea Welton,
    • Daniel E.L. Promislow,
    • James H. Thomas,
    • Matt Kaeberlein,
    • and Brian K. Kennedy
    Genome Res. April 2008 18: 564-570; Published in Advance March 13, 2008, doi:10.1101/gr.074724.107
    ...Quantitative evidence for conserved longevity pathways between divergent eukaryotic species Erica D. Smith 1 , 2 , Mitsuhiro Tsuchiya 1 , Lindsay A. Fox 1 , Nick Dang 1 , Di Hu 1 , Emily O. Kerr 1 , Elijah D. Johnston 1...
  5. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...transcripts but not of TSSs from unstable RNAs, such as long noncoding transcripts. Furthermore, using mature RNA prevents insights into transcription initiation dynamics. Therefore, nascent or newly transcribed RNA is required for detecting TSSs of unstable transcripts and quantitative analysis...
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  6. LETTER: Quantitative Assessment of Transcriptome Differences Between Brain Territories
    • Michel de Chaldée,
    • Marie-Claude Gaillard,
    • Nicolas Bizat,
    • Jean-Marie Buhler,
    • Olivier Manzoni,
    • Joël Bockaert,
    • Philippe Hantraye,
    • Emmanuel Brouillet,
    • and Jean-Marc Elalouf
    Genome Res. July 2003 13: 1646-1653; doi:10.1101/gr.1173403
    ...a microassay for serial analysis of gene expression (SAGE) to generate quantitative mRNA expression profiles of normal adult mouse striatum, nucleus accumbens, and somatosensory cortex. Comparison of these profiles revealed 135 transcripts heterogeneously distributed in the brain. Among them, a majority (78...
  7. Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
    • Jesper Eisfeldt,
    • Adam Ameur,
    • Felix Lenner,
    • Esmee Ten Berk de Boer,
    • Marlene Ek,
    • Josephine Wincent,
    • Raquel Vaz,
    • Jesper Ottosson,
    • Tord Jonson,
    • Sofie Ivarsson,
    • Sofia Thunström,
    • Alexandra Topa,
    • Simon Stenberg,
    • Anna Rohlin,
    • Anna Sandestig,
    • Margareta Nordling,
    • Pia Palmebäck,
    • Magnus Burstedt,
    • Frida Nordin,
    • Eva-Lena Stattin,
    • Maria Sobol,
    • Panagiotis Baliakas,
    • Marie-Louise Bondeson,
    • Ida Höijer,
    • Kristine Bilgrav Saether,
    • Lovisa Lovmar,
    • Hans Ehrencrona,
    • Malin Melin,
    • Lars Feuk,
    • and Anna Lindstrand
    Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
    ...using Megaruptor 3 (Diagenode). PacBio SMRTbell library construction was performed using the SMRTbell Template prep kit 3.0. SMRTbell libraries were size-selected either using AMPure beads or by the gel-based systems pippinHT (Sage Science) or SageElf (Sage Science). The library preparation procedure...
    OPEN ACCESS ARTICLE
  8. LETTER: Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast
    • Heiko Schober,
    • Véronique Kalck,
    • Miguel A. Vega-Palas,
    • Griet Van Houwe,
    • Daniel Sage,
    • Michael Unser,
    • Marc R. Gartenberg,
    • and Susan M. Gasser
    Genome Res. February 2008 18: 261-271; Published in Advance December 20, 2007, doi:10.1101/gr.6687808
    ...Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast Heiko Schober 1 , 2 , Véronique Kalck 1 , Miguel A. Vega-Palas 3 , Griet Van Houwe 2 , Daniel Sage 4 , Michael Unser 4 , Marc R...
  9. Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
    • Ilya B. Slizovskiy,
    • Nathalie Bonin,
    • Jonathan E. Bravo,
    • Peter M. Ferm,
    • Jacob Singer,
    • Christina Boucher,
    • and Noelle R. Noyes
    Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
    ...that the differences in beta-diversity observed by enrichment protocol were associated primarily with differences between TELSeq and nonenriched libraries, with smaller differences between XT and XT-HS2 libraries.Another way to evaluate composition is through a binary heatmap (Fig. 5). This analysis revealed...
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  10. Resource: MicroRNA programs in normal and aberrant stem and progenitor cells
    • Christopher P. Arnold,
    • Ruoying Tan,
    • Baiyu Zhou,
    • Si-Biao Yue,
    • Steven Schaffert,
    • Joseph R. Biggs,
    • Regis Doyonnas,
    • Miao-Chia Lo,
    • John M. Perry,
    • Valérie M. Renault,
    • Alessandra Sacco,
    • Tim Somervaille,
    • Patrick Viatour,
    • Anne Brunet,
    • Michael L. Cleary,
    • Linheng Li,
    • Julien Sage,
    • Dong-Er Zhang,
    • Helen M. Blau,
    • Caifu Chen,
    • and Chang-Zheng Chen
    Genome Res. May 2011 21: 798-810; Published in Advance March 30, 2011, doi:10.1101/gr.111385.110
    ..., Miao-Chia Lo 5 , John M. Perry 6 , Valérie M. Renault 7 , Alessandra Sacco 1 , 2 , 8 , Tim Somervaille 9 , Patrick Viatour 10 , Anne Brunet 7 , Michael L. Cleary 9 , Linheng Li 6 , 11 , Julien Sage 7 , 10...
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