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RNA quality in frozen breast cancer samples and the influence on gene expression analysis--a comparison of three evaluation methods using microcapillary electrophoresis traces.

Strand C, Enell J, Hedenfalk I, Fernö M.

BMC Mol Biol. 2007 May 22;8:38.

PMID: 17519006 [PubMed - indexed for MEDLINE]

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Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces.

Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller O, Schroeder A, Auffray C.

Nucleic Acids Res. 2005 Mar 30;33(6):e56.

PMID: 15800207 [PubMed - indexed for MEDLINE]

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Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma.

Symmans WF, Ayers M, Clark EA, Stec J, Hess KR, Sneige N, Buchholz TA, Krishnamurthy S, Ibrahim NK, Buzdar AU, Theriault RL, Rosales MF, Thomas ES, Gwyn KM, Green MC, Syed AR, Hortobagyi GN, Pusztai L.

Cancer. 2003 Jun 15;97(12):2960-71.

PMID: 12784330 [PubMed - indexed for MEDLINE]

Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology.

Weis S, Llenos IC, Dulay JR, Elashoff M, Martínez-Murillo F, Miller CL.

J Neurosci Methods. 2007 Sep 30;165(2):198-209. Epub 2007 Jun 7.

PMID: 17628689 [PubMed - indexed for MEDLINE]

Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses.

Ellis M, Davis N, Coop A, Liu M, Schumaker L, Lee RY, Srikanchana R, Russell CG, Singh B, Miller WR, Stearns V, Pennanen M, Tsangaris T, Gallagher A, Liu A, Zwart A, Hayes DF, Lippman ME, Wang Y, Clarke R.

Clin Cancer Res. 2002 May;8(5):1155-66.

PMID: 12006532 [PubMed - indexed for MEDLINE]

Optimization of the method of RNA isolation from paraffin blocks to assess gene expression in breast cancer.

Jarzab M, Rózanowski P, Kowalska M, Zebracka J, Rudnicka L, Stobiecka E, Jarzab B, Stachura J, Pawlega J.

Pol J Pathol. 2008;59(2):85-91.

PMID: 18669173 [PubMed - indexed for MEDLINE]

Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality.

Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, Mazière P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Del Rio M.

J Biotechnol. 2007 Jan 20;127(4):549-59. Epub 2006 Aug 2.

PMID: 16945445 [PubMed - indexed for MEDLINE]

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays.

Ravo M, Mutarelli M, Ferraro L, Grober OM, Paris O, Tarallo R, Vigilante A, Cimino D, De Bortoli M, Nola E, Cicatiello L, Weisz A.

Lab Invest. 2008 Apr;88(4):430-40. Epub 2008 Feb 25.

PMID: 18305565 [PubMed - indexed for MEDLINE]

Reliability and reproducibility of gene expression measurements using amplified RNA from laser-microdissected primary breast tissue with oligonucleotide arrays.

King C, Guo N, Frampton GM, Gerry NP, Lenburg ME, Rosenberg CL.

J Mol Diagn. 2005 Feb;7(1):57-64.

PMID: 15681475 [PubMed - indexed for MEDLINE]

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Global gene expression changes during neoadjuvant chemotherapy for human breast cancer.

Buchholz TA, Stivers DN, Stec J, Ayers M, Clark E, Bolt A, Sahin AA, Symmans WF, Hess KR, Kuerer HM, Valero V, Hortobagyi GN, Pusztai L.

Cancer J. 2002 Nov-Dec;8(6):461-8.

PMID: 12500855 [PubMed - indexed for MEDLINE]

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Identification of gene signatures for invasive colorectal tumor cells.

Wiese AH, Auer J, Lassmann S, Nährig J, Rosenberg R, Höfler H, Rüger R, Werner M.

Cancer Detect Prev. 2007;31(4):282-95.

PMID: 17936523 [PubMed - indexed for MEDLINE]

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Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers.

Yau C, Fedele V, Roydasgupta R, Fridlyand J, Hubbard A, Gray JW, Chew K, Dairkee SH, Moore DH, Schittulli F, Tommasi S, Paradiso A, Albertson DG, Benz CC.

Breast Cancer Res. 2007;9(5):R59.

PMID: 17850661 [PubMed - indexed for MEDLINE]

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A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays.

Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M.

BMC Genomics. 2004 Jan 6;5(1):2.

PMID: 14709180 [PubMed - indexed for MEDLINE]

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Challenges in projecting clustering results across gene expression-profiling datasets.

Lusa L, McShane LM, Reid JF, De Cecco L, Ambrogi F, Biganzoli E, Gariboldi M, Pierotti MA.