Transcriptomics,Genomics

Dataset Information

32

Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays


ABSTRACT: The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison Overall design: Expression data from two distinct reference RNA samples: Stratagene Universal Human Reference RNA (Catalog #740000) and Ambion Human Brain Reference RNA (Catalog #6050) were generated using different labeling protocols and technology platforms. We compared the results from 4 different technical protocols: Affymetrix HG-U133 Plus 2.0 array with Message Amp from Ambion labeling (protocol A), Affymetrix HG-U133 Plus 2.0 array with Ovation from NuGen labeling (protocol N), Affymetrix Gene 1.0 ST array (protocol G) and Illumina HumanRef-8 BeadChip (protocol I) with their respective labeling methods. Samples labeling and hybridization were repeated 2 times on different days with each time 2 technical replicates for a total of 4 technical replicates per condition.

REANALYSED by: GSE119128

INSTRUMENT(S): [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

SUBMITTER: Sylvain Pradervand   

PROVIDER: GSE9819 | GEO | 2008-02-01

SECONDARY ACCESSION(S): PRJNA103777

REPOSITORIES: GEO

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Publications

Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays.

Pradervand Sylvain S   Paillusson Alexandra A   Thomas Jérôme J   Weber Johann J   Wirapati Pratyaksha P   Hagenbüchle Otto O   Harshman Keith K  

BioTechniques 20080501 6


The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3' based arrays: (i) it interrogates the entire mRNA transcript, and (ii) it uses DNA targets. To assess the impact of these differences on array performance, we performed a series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both RNA and DNA targets were hybridized on HG-U133 Plus 2  ...[more]

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