BMC Genomics

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Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

Hongjuan Zhao, Trevor Hastie, Michael L Whitfield, Anne-Lise Børresen-Dale and Stefanie S Jeffrey*

BMC Genomics 2002, 3:31 doi:10.1186/1471-2164-3-31

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BioMed Central: 27 citations

Research article   Open Access

Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma

Wusheng Yan, Joanna H Shih, Jaime Rodriguez-Canales, Michael A Tangrea, Kris Ylaya, Jason Hipp, Audrey Player, Nan Hu, Alisa M Goldstein, Philip R Taylor, Michael R Emmert-Buck, Heidi S Erickson BMC Research Notes 2012, 5:73 (26 January 2012)

Research article   Open Access

Gene network analyses point to the importance of human tissue kallikreins in melanoma progression

Waleska K Martins, Gustavo H Esteves, Otávio M Almeida, Gisele G Rezze, Gilles Landman, Sarah M Marques, Alex F Carvalho, Luiz F L Reis, João P Duprat, Beatriz S Stolf BMC Medical Genomics 2011, 4:76 (27 October 2011)

Short Report   Open Access Highly Accessed

RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts

Joëlle Vermeulen, Stefaan Derveaux, Steve Lefever, Els De Smet, Katleen De Preter, Nurten Yigit, Anne De Paepe, Filip Pattyn, Frank Speleman, Jo Vandesompele BMC Research Notes 2009, 2:235 (25 November 2009)

This article is part of a collection on Quantitative real time PCR...

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A comparison of RNA amplification techniques at sub-nanogram input concentration

Julie E Lang, Mark Magbanua, Janet H Scott, G Mike Makrigiorgos, Gang Wang, Scot Federman, Laura J Esserman, John W Park, Christopher M Haqq BMC Genomics 2009, 10:326 (20 July 2009)

Methodology article   Open Access Highly Accessed

Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

Mathieu Clément-Ziza, David Gentien, Stanislas Lyonnet, Jean-Paul Thiery, Claude Besmond, Charles Decraene BMC Genomics 2009, 10:246 (26 May 2009)

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TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer

Anita Langerød, Hongjuan Zhao, Ørnulf Borgan, Jahn M Nesland, Ida RK Bukholm, Tone Ikdahl, Rolf Kåresen, Anne-Lise Børresen-Dale, Stefanie S Jeffrey Breast Cancer Research 2007, 9:R30 (15 May 2007)

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Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer

Dagmar M Kube, Cemile D Savci-Heijink, Anne-Françoise Lamblin, Farhad Kosari, George Vasmatzis, John C Cheville, Donald P Connelly, George G Klee BMC Molecular Biology 2007, 8:25 (21 March 2007)

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Discovery and validation of breast cancer subtypes

Amy V Kapp, Stefanie S Jeffrey, Anita Langerød, Anne-Lise Børresen-Dale, Wonshik Han, Dong-Young Noh, Ida RK Bukholm, Monica Nicolau, Patrick O Brown, Robert Tibshirani BMC Genomics 2006, 7:231 (11 September 2006)

A novel statistical validation method applied to five microarray datasets reveals that breast cancer tumors can be consistently classified into three subtypes: ESR1+/ERBB2-, ESR1-/ERBB2-, and ERBB2+.

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Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms

Therese Sørlie, Yulei Wang, Chunlin Xiao, Hilde Johnsen, Bjørn Naume, Raymond R Samaha, Anne-Lise Børresen-Dale BMC Genomics 2006, 7:127 (26 May 2006)

Gene expression profiles of early breast tumors validate recognition of two clinically relevant cancer subtypes across three microarray platforms; a minimal set of 54 signature genes discriminate best between luminal A and basal-like subtypes.

Research article   Open Access

The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression

Simon Hughes, Maisa Yoshimoto, Ben Beheshti, Richard S Houlston, Jeremy A Squire, Andrew Evans BMC Genomics 2006, 7:65 (30 March 2006)

Research   Open Access Highly Accessed

Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level

Tatiana Subkhankulova, Frederick J Livesey Genome Biology 2006, 7:R18 (7 March 2006)

Comparison of the performance of three methods for amplifying single-cell amounts of RNA for use in expression profiling shows that PCT amplification is more reliable than linear amplification.

Research article   Open Access

Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles

Elza C de Bruin, Simone van de Pas, Esther H Lips, Ronald van Eijk, Minke MC van der Zee, Marcel Lombaerts, Tom van Wezel, Corrie AM Marijnen, J Han JM van Krieken, Jan Medema, Cornelis JH van de Velde, Paul HC Eilers, Lucy TC Peltenburg BMC Genomics 2005, 6:142 (14 October 2005)

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Differential gene expression in anatomical compartments of the human eye

Jennifer J Diehn, Maximilian Diehn, Michael F Marmor, Patrick O Brown Genome Biology 2005, 6:R74 (17 August 2005)

DNA microarrays (representing approximately 30,000 human genes) were used to analyze gene expression in six different human eye compartments, revealing candidate genes for diseases affecting the cornea, lens and retina.

Review   Open Access

RNA amplification for successful gene profiling analysis

Ena Wang Journal of Translational Medicine 2005, 3:28 (25 July 2005)

Methodology article   Open Access Highly Accessed

A robust method for the amplification of RNA in the sense orientation

Nicholas F Marko, Bryan Frank, John Quackenbush, Norman H Lee BMC Genomics 2005, 6:27 (1 March 2005)

Research   Open Access Highly Accessed

cDNA microarray analysis of bovine embryo gene expression profiles during the pre-implantation period

Koichi Ushizawa, Chandana B Herath, Kanako Kaneyama, Satoshi Shiojima, Akira Hirasawa, Toru Takahashi, Kei Imai, Kazuhiko Ochiai, Tomoyuki Tokunaga, Yukio Tsunoda, Gozoh Tsujimoto, Kazuyoshi Hashizume Reproductive Biology and Endocrinology 2004, 2:77 (24 November 2004)

Methodology article   Open Access Highly Accessed

Evaluation of sense-strand mRNA amplification by comparative quantitative PCR

Loyal A Goff, Jessica Bowers, Jaime Schwalm, Kevin Howerton, Robert C Getts, Ronald P Hart BMC Genomics 2004, 5:76 (6 October 2004)

Research article   Open Access

A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue

Shanaz H Dairkee, Youngran Ji, Yong Ben, Dan H Moore, Zhenhang Meng, Stefanie S Jeffrey BMC Genomics 2004, 5:47 (19 July 2004)

Research article   Open Access

Microarray analysis in clinical oncology: pre-clinical optimization using needle core biopsies from xenograft tumors

Elizabeth M Goley, Soni J Anderson, Cynthia Ménard, Eric Chuang, Xing Lü, Philip J Tofilon, Kevin Camphausen BMC Cancer 2004, 4:20 (19 May 2004)

Research article   Open Access

Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments

Jörg Schneider, Andreas Buneß, Wolfgang Huber, Joachim Volz, Petra Kioschis, Mathias Hafner, Annemarie Poustka, Holger Sültmann BMC Genomics 2004, 5:29 (30 April 2004)

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Genetic alteration and gene expression modulation during cancer progression

Cathie Garnis, Timon PH Buys, Wan L Lam Molecular Cancer 2004, 3:9 (22 March 2004)

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Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

Ali Naderi, Ahmed A Ahmed, Nuno L Barbosa-Morais, Samuel Aparicio, James D Brenton, Carlos Caldas BMC Genomics 2004, 5:9 (30 January 2004)

Methodology article   Open Access

Evaluation of five different cDNA labeling methods for microarrays using spike controls

Azadeh Badiee, Hans Eiken, Vidar M Steen, Roger Løvlie BMC Biotechnology 2003, 3:23 (11 December 2003)

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Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations

Andrej-Nikolai Spiess, Nadine Mueller, Richard Ivell BMC Genomics 2003, 4:44 (10 November 2003)

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The diagnosis and management of pre-invasive breast disease: Promise of new technologies in understanding pre-invasive breast lesions

Stefanie S Jeffrey, Jonathan R Pollack Breast Cancer Res 2003, 5:320-328 (9 October 2003)

This article is part of a collection on The diagnosis and...

Methodology article   Open Access Highly Accessed

Development and validation of a T7 based linear amplification for genomic DNA

Chih Long Liu, Stuart L Schreiber, Bradley E Bernstein BMC Genomics 2003, 4:19 (9 May 2003)

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Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance

Vigdis Nygaard, Anders Løland, Marit Holden, Mette Langaas, Håvard Rue, Fang Liu, Ola Myklebost, Øystein Fodstad, Eivind Hovig, Birgitte Smith-Sørensen BMC Genomics 2003, 4:11 (23 March 2003)