Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice

ABSTRACT: The aim of the present study was to compare, on a statistical basis, the performance of different microarray platforms to detect differences in gene expression in a realistic and challenging biological setting. Gene expression profiles in the hippocampus of five wild-type and five transgenic Î´C-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina and home-spotted oligonucleotide arrays. We observed considerable overlap between the different platforms, the overlap being better detectable with significance level-based ranking than with a p-value based cut-off. Confirming the qualitative agreement between platforms, Pathway analysis consistently demonstrated aberrances in GABA-ergic signalling in the transgenic mice, even though pathways were represented by only partially overlapping genes on the different platforms. Keywords: microarray platform comparison 5 biological replicates for each experimental group were analyzed on each of the five platforms. For two-color arrays a dye swap was performed. ABI_raw_data.csv contains the raw data for GSM206638 to GSM206647. Illumina_raw_data.csv contains the raw data for GSM206887 to GSM206896. In these files, the sample identifiers are included in the column headers.

ORGANISM(S): Mus musculus

SUBMITTER: P Pedotti

PROVIDER: E-GEOD-8349 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Pedotti Paola P 't Hoen Peter A C PA Vreugdenhil Erno E Schenk Geert J GJ Vossen Rolf Ham RH Ariyurek Yavuz Y de Hollander Mattias M Kuiper Rowan R van Ommen Gertjan J B GJ den Dunnen Johan T JT Boer Judith M JM de Menezes Renée X RX

BMC genomics 20080310

<h4>Background</h4>The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle.<h4>Results</h4>Gene expression profiles in the hippocampus of five wild-type and five transgenic deltaC-doublecortin-like kinase mi ...[more]

PMID: 18331641

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Project description:We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for sequence discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcriptlevel profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. The well-characterized reference RNA samples A (pooled cell lines) and B (human brain) from the MAQC consortium, adding spike-ins of synthetic RNA from the External RNA Control Consortium (ERCC). Samples C and D were then constructed by combining A and B in known mixing ratios, 3:1 and 1:3, respectively. All samples were distributed to several independent sites for RNA-Seq library construction and profiling by Illumina HiSeq 2000 and LifeTech SOLiD 5500 platforms. Also, vendors created their own cDNA libraries that were then distributed to each test site, in order to examine the degree of a M-bM-^@M-^\site effectM-bM-^@M-^] that was independent of the library preparation process. To support an assessment of gene models, samples A and B were also sequenced at independent sites by the Roche 454 platform, providing longer reads. For comparison to other technologies, these data were also compared to the MAQC-I Affymetrix U133 Plus2 microarray, several current microarray platforms, and also assessed by 20,801 PrimePCR reactions.

Dataset Information

Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice

Publications

Can subtle changes in gene expression be consistently detected with different microarray platforms?

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