Literature DB >> 21326892

Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts.

Oskar Bruning1, Xiaolian Yuan, Wendy Rodenburg, Wendy Bruins, Conny T van Oostrom, Han Rauwerda, Floyd Ra Wittink, Martijs J Jonker, Annemieke de Vries, Timo M Breit.   

Abstract

Reanalysis of our UV study of p53-mutant mouse embryonic fibroblasts revealed an intriguing orchestration of massive transcriptome responses. However, close scrutiny of the data uncovered an affected mRNA/rRNA ratio, effectively inhibiting valid data analysis. UV-dose range-finding showed low-dose UV specific- and high-dose stress-related responses, which represent a plea for UV dose range-finding in experimental design.

Entities:  

Year:  2010        PMID： 21326892      PMCID： PMC3023578          DOI： 10.4161/trns.1.3.13487

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  31 in total

1.  Evaluation of DNA microarray results with quantitative gene expression platforms.

Authors:  Roger D Canales; Yuling Luo; James C Willey; Bradley Austermiller; Catalin C Barbacioru; Cecilie Boysen; Kathryn Hunkapiller; Roderick V Jensen; Charles R Knight; Kathleen Y Lee; Yunqing Ma; Botoul Maqsodi; Adam Papallo; Elizabeth Herness Peters; Karen Poulter; Patricia L Ruppel; Raymond R Samaha; Leming Shi; Wen Yang; Lu Zhang; Federico M Goodsaid
Journal:  Nat Biotechnol       Date:  2006-09       Impact factor: 54.908

2.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:  Leming Shi; Laura H Reid; Wendell D Jones; Richard Shippy; Janet A Warrington; Shawn C Baker; Patrick J Collins; Francoise de Longueville; Ernest S Kawasaki; Kathleen Y Lee; Yuling Luo; Yongming Andrew Sun; James C Willey; Robert A Setterquist; Gavin M Fischer; Weida Tong; Yvonne P Dragan; David J Dix; Felix W Frueh; Frederico M Goodsaid; Damir Herman; Roderick V Jensen; Charles D Johnson; Edward K Lobenhofer; Raj K Puri; Uwe Schrf; Jean Thierry-Mieg; Charles Wang; Mike Wilson; Paul K Wolber; Lu Zhang; Shashi Amur; Wenjun Bao; Catalin C Barbacioru; Anne Bergstrom Lucas; Vincent Bertholet; Cecilie Boysen; Bud Bromley; Donna Brown; Alan Brunner; Roger Canales; Xiaoxi Megan Cao; Thomas A Cebula; James J Chen; Jing Cheng; Tzu-Ming Chu; Eugene Chudin; John Corson; J Christopher Corton; Lisa J Croner; Christopher Davies; Timothy S Davison; Glenda Delenstarr; Xutao Deng; David Dorris; Aron C Eklund; Xiao-hui Fan; Hong Fang; Stephanie Fulmer-Smentek; James C Fuscoe; Kathryn Gallagher; Weigong Ge; Lei Guo; Xu Guo; Janet Hager; Paul K Haje; Jing Han; Tao Han; Heather C Harbottle; Stephen C Harris; Eli Hatchwell; Craig A Hauser; Susan Hester; Huixiao Hong; Patrick Hurban; Scott A Jackson; Hanlee Ji; Charles R Knight; Winston P Kuo; J Eugene LeClerc; Shawn Levy; Quan-Zhen Li; Chunmei Liu; Ying Liu; Michael J Lombardi; Yunqing Ma; Scott R Magnuson; Botoul Maqsodi; Tim McDaniel; Nan Mei; Ola Myklebost; Baitang Ning; Natalia Novoradovskaya; Michael S Orr; Terry W Osborn; Adam Papallo; Tucker A Patterson; Roger G Perkins; Elizabeth H Peters; Ron Peterson; Kenneth L Philips; P Scott Pine; Lajos Pusztai; Feng Qian; Hongzu Ren; Mitch Rosen; Barry A Rosenzweig; Raymond R Samaha; Mark Schena; Gary P Schroth; Svetlana Shchegrova; Dave D Smith; Frank Staedtler; Zhenqiang Su; Hongmei Sun; Zoltan Szallasi; Zivana Tezak; Danielle Thierry-Mieg; Karol L Thompson; Irina Tikhonova; Yaron Turpaz; Beena Vallanat; Christophe Van; Stephen J Walker; Sue Jane Wang; Yonghong Wang; Russ Wolfinger; Alex Wong; Jie Wu; Chunlin Xiao; Qian Xie; Jun Xu; Wen Yang; Liang Zhang; Sheng Zhong; Yaping Zong; William Slikker
Journal:  Nat Biotechnol       Date:  2006-09       Impact factor: 54.908

3.  DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation.

Authors:  Manuel J Muñoz; M Soledad Pérez Santangelo; Maria P Paronetto; Manuel de la Mata; Federico Pelisch; Stéphanie Boireau; Kira Glover-Cutter; Claudia Ben-Dov; Matías Blaustein; Juan J Lozano; Gregory Bird; David Bentley; Edouard Bertrand; Alberto R Kornblihtt
Journal:  Cell       Date:  2009-05-15       Impact factor: 41.582

4.  Dissecting the regulatory circuitry of a eukaryotic genome.

Authors:  F C Holstege; E G Jennings; J J Wyrick; T I Lee; C J Hengartner; M R Green; T R Golub; E S Lander; R A Young
Journal:  Cell       Date:  1998-11-25       Impact factor: 41.582

5.  Gene expression profiling predicts clinical outcome of breast cancer.

Authors:  Laura J van 't Veer; Hongyue Dai; Marc J van de Vijver; Yudong D He; Augustinus A M Hart; Mao Mao; Hans L Peterse; Karin van der Kooy; Matthew J Marton; Anke T Witteveen; George J Schreiber; Ron M Kerkhoven; Chris Roberts; Peter S Linsley; René Bernards; Stephen H Friend
Journal:  Nature       Date:  2002-01-31       Impact factor: 49.962

6.  Regulation of human skin pigmentation in situ by repetitive UV exposure: molecular characterization of responses to UVA and/or UVB.

Authors:  Wonseon Choi; Yoshinori Miyamura; Rainer Wolber; Christoph Smuda; William Reinhold; Hongfang Liu; Ludger Kolbe; Vincent J Hearing
Journal:  J Invest Dermatol       Date:  2010-02-11       Impact factor: 8.551

7.  Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models.

Authors:  Martijs J Jonker; Oskar Bruning; Maarten van Iterson; Mirjam M Schaap; Tessa V van der Hoeven; Harry Vrieling; Rudolf B Beems; Annemieke de Vries; Harry van Steeg; Timo M Breit; Mirjam Luijten
Journal:  Carcinogenesis       Date:  2009-08-20       Impact factor: 4.944

8.  Increased sensitivity to UV radiation in mice with a p53 point mutation at Ser389.

Authors:  Wendy Bruins; Edwin Zwart; Laura D Attardi; Tomoo Iwakuma; Esther M Hoogervorst; Rudolf B Beems; Barbara Miranda; Conny T M van Oostrom; Jolanda van den Berg; Gerard J van den Aardweg; Guillermina Lozano; Harry van Steeg; Tyler Jacks; Annemieke de Vries
Journal:  Mol Cell Biol       Date:  2004-10       Impact factor: 4.272

9.  The absence of Ser389 phosphorylation in p53 affects the basal gene expression level of many p53-dependent genes and alters the biphasic response to UV exposure in mouse embryonic fibroblasts.

Authors:  Wendy Bruins; Oskar Bruning; Martijs J Jonker; Edwin Zwart; Tessa V van der Hoeven; Jeroen L A Pennings; Han Rauwerda; Annemieke de Vries; Timo M Breit
Journal:  Mol Cell Biol       Date:  2008-01-14       Impact factor: 4.272

10.  Global transcriptional responses of fission yeast to environmental stress.

Authors:  Dongrong Chen; W Mark Toone; Juan Mata; Rachel Lyne; Gavin Burns; Katja Kivinen; Alvis Brazma; Nic Jones; Jürg Bähler
Journal:  Mol Biol Cell       Date:  2003-01       Impact factor: 4.138
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  4 in total

1.  Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.

Authors:  Jeffrey S Buzby; Shirley A Williams; Lana Schaffer; Steven R Head; Diane J Nugent
Journal:  Cancer Genet       Date:  2017-01-09

Review 2.  Valuable lessons-learned in transcriptomics experimentation.

Authors:  Oskar Bruning; Han Rauwerda; Rob J Dekker; Wim C de Leeuw; Paul F K Wackers; Wim A Ensink; Martijs J Jonker; Timo M Breit
Journal:  Transcription       Date:  2015

3.  Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment.

Authors:  Oskar Bruning; Wendy Rodenburg; Paul F K Wackers; Conny van Oostrom; Martijs J Jonker; Rob J Dekker; Han Rauwerda; Wim A Ensink; Annemieke de Vries; Timo M Breit
Journal:  PLoS One       Date:  2016-01-20       Impact factor: 3.240

4.  A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure.

Authors:  Oskar Bruning; Wendy Rodenburg; Conny T van Oostrom; Martijs J Jonker; Mark de Jong; Rob J Dekker; Han Rauwerda; Wim A Ensink; Annemieke de Vries; Timo M Breit
Journal:  PLoS One       Date:  2014-05-13       Impact factor: 3.240
  4 in total

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