Analysis of Affymetrix GeneChip® data using amplified RNA

Leslie Cope, Scott M. Hartman, Hinrich W H Göhlmann, Jay P. Tiesman, Rafael A. Irizarry

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)165-170
Number of pages6
JournalBioTechniques
Volume40
Issue number2
DOIs
StatePublished - Feb 2006

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Labeling
RNA
Transcription
Complementary DNA
Microdissection
Amplification
Experiments
In Vitro Techniques
Data Accuracy

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Cope, L., Hartman, S. M., Göhlmann, H. W. H., Tiesman, J. P., & Irizarry, R. A. (2006). Analysis of Affymetrix GeneChip® data using amplified RNA. BioTechniques, 40(2), 165-170. https://doi.org/10.2144/000112057

Analysis of Affymetrix GeneChip® data using amplified RNA. / Cope, Leslie; Hartman, Scott M.; Göhlmann, Hinrich W H; Tiesman, Jay P.; Irizarry, Rafael A.

In: BioTechniques, Vol. 40, No. 2, 02.2006, p. 165-170.

Research output: Contribution to journalArticle

Cope, L, Hartman, SM, Göhlmann, HWH, Tiesman, JP & Irizarry, RA 2006, 'Analysis of Affymetrix GeneChip® data using amplified RNA', BioTechniques, vol. 40, no. 2, pp. 165-170. https://doi.org/10.2144/000112057
Cope L, Hartman SM, Göhlmann HWH, Tiesman JP, Irizarry RA. Analysis of Affymetrix GeneChip® data using amplified RNA. BioTechniques. 2006 Feb;40(2):165-170. https://doi.org/10.2144/000112057
Cope, Leslie ; Hartman, Scott M. ; Göhlmann, Hinrich W H ; Tiesman, Jay P. ; Irizarry, Rafael A. / Analysis of Affymetrix GeneChip® data using amplified RNA. In: BioTechniques. 2006 ; Vol. 40, No. 2. pp. 165-170.
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