Browsing by Author "Goff, Loyal"

Now showing items 1-7 of 7

    • Differential Gene and Transcript Expression Analysis of RNA-seq Experiments with TopHat and Cufflinks 

      Trapnell, Cole; Roberts, Adam; Goff, Loyal; Pertea, Geo; Kim, Daehwan; Kelley, David Roy; Pimentel, Harold; Salzberg, Steven L.; Rinn, John L; Pachter, Lior (Nature Publishing Group, 2012)
      Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments ...

    • DNMT1-interacting RNAs block gene specific DNA methylation 

      Di Ruscio, Annalisa; Ebralidze, Alexander K.; Benoukraf, Touati; Amabile, Giovanni; Goff, Loyal A.; Terragni, Joylon; Figueroa, Maria Eugenia; De Figureido Pontes, Lorena Lobo; Alberich-Jorda, Meritxell; Zhang, Pu; Wu, Mengchu; D’Alò, Francesco; Melnick, Ari; Leone, Giuseppe; Ebralidze, Konstantin K.; Pradhan, Sriharsa; Rinn, John L.; Tenen, Daniel G. (2013)
      Summary DNA methylation was described almost a century ago. However, the rules governing its establishment and maintenance remain elusive. Here, we present data demonstrating that active transcription regulates levels of ...

    • The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan 

      Kotzin, Jonathan J.; Spencer, Sean Paul; McCright, Sam J.; Kumar, Dinesh B. Uthaya; Collet, Magalie A.; Mowel, Walter K.; Elliott, Ellen N.; Uyar, Asli; Makiya, Michelle A.; Dunagin, Margaret C.; Harman, Christian C.D.; Virtue, Anthony T.; Zhu, Stella; Bailis, Will; Stein, Judith; Hughes, Cynthia; Raj, Arjun; Wherry, E. John; Goff, Loyal; Klion, Amy D.; Rinn, John L; Williams, Adam; Flavell, Richard A.; Henao-Mejia, Jorge (Springer Nature, 2016)
      Neutrophils, eosinophils and “classical” monocytes collectively account for ~70% ofhuman blood leukocytes and are among the shortest-lived cells in the body. Precise regulation of the lifespan of these myeloid cells is ...

    • Long Noncoding RNAs Regulate Adipogenesis 

      Sun, Lei; Goff, Loyal Andrew; Trapnell, Cole; Alexander, Ryan Kendall; Lo, Kinyui Alice; Hacisuleyman, Ezgi; Sauvageau, Martin; Tazon-Vega, Barbara; Kelley, David Roy; Hendrickson, David Gillis; Yuan, Bingbing; Kellis, Manolis; Lodish, Harvey F.; Rinn, John L (Proceedings of the National Academy of Sciences, 2013)
      The prevalence of obesity has led to a surge of interest in understanding the detailed mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and microRNAs have been implicated in adipocyte development, ...

    • Multiple knockout mouse models reveal lincRNAs are required for life and brain development 

      Sauvageau, Martin; Goff, Loyal A; Lodato, Simona; Bonev, Boyan; Groff, Abigail F; Gerhardinger, Chiara; Sanchez-Gomez, Diana B; Hacisuleyman, Ezgi; Li, Eric; Spence, Matthew; Liapis, Stephen C; Mallard, William; Morse, Michael; Swerdel, Mavis R; D’Ecclessis, Michael F; Moore, Jennifer C; Lai, Venus; Gong, Guochun; Yancopoulos, George D; Frendewey, David; Kellis, Manolis; Hart, Ronald P; Valenzuela, David M; Arlotta, Paola; Rinn, John L (eLife Sciences Publications, Ltd, 2013)
      Many studies are uncovering functional roles for long noncoding RNAs (lncRNAs), yet few have been tested for in vivo relevance through genetic ablation in animal models. To investigate the functional relevance of lncRNAs ...

    • RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome 

      Silverman, Ian M; Li, Fan; Alexander, Anissa; Goff, Loyal; Trapnell, Cole; Rinn, John L; Gregory, Brian D (BioMed Central, 2014)
      Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP–RNA interactions. Here, we describe PIP-seq, a ...

    • Topological Organization of Multi-chromosomal Regions by Firre 

      Hacisuleyman, Ezgi; Goff, Loyal A.; Trapnell, Cole; Williams, Adam; Henao-Mejia, Jorge; Sun, Lei; McClanahan, Patrick; Hendrickson, David G.; Sauvageau, Martin; Kelley, David R.; Morse, Michael; Engreitz, Jesse; Lander, Eric S.; Guttman, Mitch; Lodish, Harvey F.; Flavell, Richard; Raj, Arjun; Rinn, John L. (2014)
      RNA is known to be an abundant and important structural component of the nuclear matrix, including long noncoding RNAs (lncRNA). Yet the molecular identities, functional roles, and localization dynamics of lncRNAs that ...