Volume 32 Issue 9, September 2014

Volume 32 Issue 9

RNA-seq five ways. Research in this Focus issue evaluates the performance of RNA sequencing with an emphasis on large-scale studies involving data generated using multiple sequencing sites, platforms or protocols (pp 903, 915, 926, 888 and 896). Credit: Sam Shlomo Spaeth.

Editorial

  • Editorial |

    Studies from the RNA Sequencing Quality Control (SEQC) initiative exemplify the kind of experimental groundwork needed to expand RNA-seq into a broader array of basic and translational applications.

News

News Feature

  • News Feature |

    Is the imminent release of the database of industry's 'gifts' to doctors cause for concern or celebration? Charles Schmidt investigates.

    • Charles Schmidt

Bioentrepreneur

Correspondence

Commentary

  • Commentary |

    The reliability of scientific research is under scrutiny. A recently convened working group proposes cultural adjustments to incentivize better research practices.

    • Marcus Munafò
    • , Simon Noble
    • , William J Browne
    • , Dani Brunner
    • , Katherine Button
    • , Joaquim Ferreira
    • , Peter Holmans
    • , Douglas Langbehn
    • , Glyn Lewis
    • , Martin Lindquist
    • , Kate Tilling
    • , Eric-Jan Wagenmakers
    •  & Robi Blumenstein
  • Commentary |

    Gene therapy companies that pursue high, one-time payments for their products risk a backlash from payors. A better solution may lie in a pay-for-performance model.

    • Troyen A Brennan
    •  & James M Wilson

Patents

News & Views

Analysis

Article

  • Article |

    The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.

    • Zhenqiang Su
    • , Paweł P Łabaj
    • , Sheng Li
    • , Jean Thierry-Mieg
    • , Danielle Thierry-Mieg
    • , Wei Shi
    • , Charles Wang
    • , Gary P Schroth
    • , Robert A Setterquist
    • , John F Thompson
    • , Wendell D Jones
    • , Wenzhong Xiao
    • , Weihong Xu
    • , Roderick V Jensen
    • , Reagan Kelly
    • , Joshua Xu
    • , Ana Conesa
    • , Cesare Furlanello
    • , Hanlin Gao
    • , Huixiao Hong
    • , Nadereh Jafari
    • , Stan Letovsky
    • , Yang Liao
    • , Fei Lu
    • , Edward J Oakeley
    • , Zhiyu Peng
    • , Craig A Praul
    • , Javier Santoyo-Lopez
    • , Andreas Scherer
    • , Tieliu Shi
    • , Gordon K Smyth
    • , Frank Staedtler
    • , Peter Sykacek
    • , Xin-Xing Tan
    • , E Aubrey Thompson
    • , Jo Vandesompele
    • , May D Wang
    • , Jian Wang
    • , Russell D Wolfinger
    • , Jiri Zavadil
    • , Scott S Auerbach
    • , Wenjun Bao
    • , Hans Binder
    • , Thomas Blomquist
    • , Murray H Brilliant
    • , Pierre R Bushel
    • , Weimin Cai
    • , Jennifer G Catalano
    • , Ching-Wei Chang
    • , Tao Chen
    • , Geng Chen
    • , Rong Chen
    • , Marco Chierici
    • , Tzu-Ming Chu
    • , Djork-Arné Clevert
    • , Youping Deng
    • , Adnan Derti
    • , Viswanath Devanarayan
    • , Zirui Dong
    • , Joaquin Dopazo
    • , Tingting Du
    • , Hong Fang
    • , Yongxiang Fang
    • , Mario Fasold
    • , Anita Fernandez
    • , Matthias Fischer
    • , Pedro Furió-Tari
    • , James C Fuscoe
    • , Florian Caimet
    • , Stan Gaj
    • , Jorge Gandara
    • , Huan Gao
    • , Weigong Ge
    • , Yoichi Gondo
    • , Binsheng Gong
    • , Meihua Gong
    • , Zhuolin Gong
    • , Bridgett Green
    • , Chao Guo
    • , Lei Guo
    • , Li-Wu Guo
    • , James Hadfield
    • , Jan Hellemans
    • , Sepp Hochreiter
    • , Meiwen Jia
    • , Min Jian
    • , Charles D Johnson
    • , Suzanne Kay
    • , Jos Kleinjans
    • , Samir Lababidi
    • , Shawn Levy
    • , Quan-Zhen Li
    • , Li Li
    • , Li Li
    • , Peng Li
    • , Yan Li
    • , Haiqing Li
    • , Jianying Li
    • , Shiyong Li
    • , Simon M Lin
    • , Francisco J López
    • , Xin Lu
    • , Heng Luo
    • , Xiwen Ma
    • , Joseph Meehan
    • , Dalila B Megherbi
    • , Nan Mei
    • , Bing Mu
    • , Baitang Ning
    • , Akhilesh Pandey
    • , Javier Pérez-Florido
    • , Roger G Perkins
    • , Ryan Peters
    • , John H Phan
    • , Mehdi Pirooznia
    • , Feng Qian
    • , Tao Qing
    • , Lucille Rainbow
    • , Philippe Rocca-Serra
    • , Laure Sambourg
    • , Susanna-Assunta Sansone
    • , Scott Schwartz
    • , Ruchir Shah
    • , Jie Shen
    • , Todd M Smith
    • , Oliver Stegle
    • , Nancy Stralis-Pavese
    • , Elia Stupka
    • , Yutaka Suzuki
    • , Lee T Szkotnicki
    • , Matthew Tinning
    • , Bimeng Tu
    • , Joost van Delft
    • , Alicia Vela-Boza
    • , Elisa Venturini
    • , Stephen J Walker
    • , Liqing Wan
    • , Wei Wang
    • , Jinhui Wang
    • , Jun Wang
    • , Eric D Wieben
    • , James C Willey
    • , Po-Yen Wu
    • , Jiekun Xuan
    • , Yong Yang
    • , Zhan Ye
    • , Ye Yin
    • , Ying Yu
    • , Yate-Ching Yuan
    • , John Zhang
    • , Ke K Zhang
    • , Wenqian Zhang
    • , Wenwei Zhang
    • , Yanyan Zhang
    • , Chen Zhao
    • , Yuanting Zheng
    • , Yiming Zhou
    • , Paul Zumbo
    • , Weida Tong
    • , David P Kreil
    • , Christopher E Mason
    •  & Leming Shi
  • Article |

    For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA- depletion enables effective analysis of degraded RNA samples.

    • Sheng Li
    • , Scott W Tighe
    • , Charles M Nicolet
    • , Deborah Grove
    • , Shawn Levy
    • , William Farmerie
    • , Agnes Viale
    • , Chris Wright
    • , Peter A Schweitzer
    • , Yuan Gao
    • , Dewey Kim
    • , Joe Boland
    • , Belynda Hicks
    • , Ryan Kim
    • , Sagar Chhangawala
    • , Nadereh Jafari
    • , Nalini Raghavachari
    • , Jorge Gandara
    • , Natàlia Garcia-Reyero
    • , Cynthia Hendrickson
    • , David Roberson
    • , Jeffrey A Rosenfeld
    • , Todd Smith
    • , Jason G Underwood
    • , May Wang
    • , Paul Zumbo
    • , Don A Baldwin
    • , George S Grills
    •  & Christopher E Mason
  • Article |

    A comparison of RNA-seq and microarray data from samples treated with diverse drugs highlights a dependency of cross-platform concordance on treatment effect.

    • Charles Wang
    • , Binsheng Gong
    • , Pierre R Bushel
    • , Jean Thierry-Mieg
    • , Danielle Thierry-Mieg
    • , Joshua Xu
    • , Hong Fang
    • , Huixiao Hong
    • , Jie Shen
    • , Zhenqiang Su
    • , Joe Meehan
    • , Xiaojin Li
    • , Lu Yang
    • , Haiqing Li
    • , Paweł P Łabaj
    • , David P Kreil
    • , Dalila Megherbi
    • , Stan Gaj
    • , Florian Caiment
    • , Joost van Delft
    • , Jos Kleinjans
    • , Andreas Scherer
    • , Viswanath Devanarayan
    • , Jian Wang
    • , Yong Yang
    • , Hui-Rong Qian
    • , Lee J Lancashire
    • , Marina Bessarabova
    • , Yuri Nikolsky
    • , Cesare Furlanello
    • , Marco Chierici
    • , Davide Albanese
    • , Giuseppe Jurman
    • , Samantha Riccadonna
    • , Michele Filosi
    • , Roberto Visintainer
    • , Ke K Zhang
    • , Jianying Li
    • , Jui-Hua Hsieh
    • , Daniel L Svoboda
    • , James C Fuscoe
    • , Youping Deng
    • , Leming Shi
    • , Richard S Paules
    • , Scott S Auerbach
    •  & Weida Tong

Letter

Erratum

Corrigendum

Careers and Recruitment

In This Issue

Focus

  • Focus |

    RNA sequencing quality control (SEQC)

    This focus presents the results of the RNA Sequencing Quality Control (SEQC) project of the MicroArray Quality Control (MAQC) Consortium that sought to evaluate the comparability of RNA-seq data from many different laboratories and of assessing different sequencing platforms and data analysis approaches and their performance compared with DNA microarrays. Ultimately, these multi-platform, cross-site studies will enable RNA-seq to be applied more broadly in analyzing large cohorts for discovery research and clinical use.