PMID: 16526405Mar 11, 2006Paper

Analysis of Affymetrix GeneChip data using amplified RNA

BioTechniques
Leslie M CopeRafael A Irizarry

Abstract

When small biological samples are collected by microdissection or other methods, amplification techniques are required to provide sufficient target for hybridization to expression arrays. One such technique is to perform two successive rounds of T7-based in vitro transcription. However the use of random primers, required to regenerate cDNA from the first round of transcription, results in shortened copies of cDNA from which the 5' end is missing. In this paper we describe an experiment designed to compare the quality of data obtained from labeling small RNA samples using the Affymetrix Two-Cycle Eukaryotic. Target Labeling procedure to that of data obtained using the One-Cycle Eukaryotic Target Labeling protocol. We utilized different preprocessing algorithms to compare the data generated using both labeling methods and present a new algorithm that improves upon existing ones in this setting.

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Citations

Oct 31, 2006·Omics : a Journal of Integrative Biology·Steffen Heber, Beate Sick
Jul 14, 2010·Genome Biology and Evolution·Thomas GigerSvante Pääbo
May 22, 2007·BMC Biotechnology·William LonerganSuzanne D Vernon
Nov 19, 2010·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Krishna H ZivrajChristine E Holt
May 9, 2007·Nanotechnology·Jason ReedJames K Gimzewski
Feb 7, 2007·Journal of Neuroendocrinology·T T ChuS C Sealfon
Apr 17, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Weibo XieQifa Zhang
Feb 24, 2006·Applied Microbiology and Biotechnology·Ken MatsuiMitsuyoshi Ueda
Jul 1, 2011·European Journal of Applied Physiology·Dmitry A SakharovAnatoly I Grigoriev
Oct 3, 2007·Genes, Chromosomes & Cancer·Derek L StirewaltJerald P Radich
Oct 12, 2007·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jordan J FeldMichael W Fried

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