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Comparative analysis of a 3′ end tag PCR and a linear RNA amplification approach for microarray analysis

Paper ID Volume ID Publish Year Pages File Format Full-Text
25513 43578 2007 9 PDF Available
Title
Comparative analysis of a 3′ end tag PCR and a linear RNA amplification approach for microarray analysis
Abstract

BackgroundVarious types of amplification techniques have been developed in order to enable microarray gene expression analysis when the amount of starting material is limited. The two main strategies are linear amplification, using in vitro transcription, and exponential amplification, based on PCR. We have evaluated the performance of a linear and an in-house developed exponential amplification protocol that relies on 3′ end tag sequences. We used 100 ng total RNA as starting material for amplification and compared the results with data from hybridizations with unamplified mRNA and total RNA.ResultsPreservation of expression ratios after amplification was examined comparing log2 ratios obtained with amplification protocols to those obtained with standard labelling of mRNA. The Pearson correlations were 0.61 and 0.84, respectively, for the two linear amplification replicates and 0.76 and 0.80 for the two exponential amplification replicates. The correlations between repeated amplifications was 0.82 with the exponential method and 0.63 with the linear, indicating a better reproducibility with the PCR-based approach.ConclusionBoth amplification methods generated results in agreement with unamplified material. In this study, the PCR-based method was more reproducible than in vitro transcription amplification. Advantages with the in-house developed method are the lower cost since it is non-commercial and that the PCR generated product offers compatibility with both sense and antisense arrays.

Keywords
Microarray; Linear amplification; Exponential amplification; RNA amplification; In vitro transcription; PCR
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Comparative analysis of a 3′ end tag PCR and a linear RNA amplification approach for microarray analysis
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 127, Issue 4, 20 January 2007, Pages 638–646
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us