Dataset Information

A Comparison of microarray and MPSS Technology Platforms for Expression Analysis of Arabidopsis

ABSTRACT: A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent For the comparison, 11 different samples were used: Callus, Inforescence, Leaf, Root, Silique, Afamous Inflorescence, Ap1-10 Inflorescence, Ap3-6 Inflorescence, Sup/Ap1 Inflorescence, Leaves SA 4 hr and Leaves SA 52 hr. For details about samples, see Meyers Lab (http://mpss.udel.edu/at). All RNA samples were created in Meyers Lab. MPSS experiments were performed in Meyers Lab. Affymetrix experiments were performed in St. Clair Lab (http://stclairlab.ucdavis.edu/). Agilent experiments were performed by Sean J Coughlan from Agilent (http://www.agilent.com/). Two replicates for each samples were used in Affymetrix platform except Silique sample. Two replicates for each samples were used in Agilent platform.

OTHER RELATED OMICS DATASETS IN: PRJNA102467

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Richard W Michelmore Blake C Meyers Sean J Coughlan Dina A St.Clair Vikas Agrawal Magnus Rattray Marilyn A West Junfeng Chen

PROVIDER: E-GEOD-8994 | ArrayExpress | 2007-09-14

SECONDARY ACCESSION(S): GSE8994PRJNA102467

REPOSITORIES: GEO, ArrayExpress

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			Action	DRS
	E-GEOD-8994.README.txt	Txt
	E-GEOD-8994.hyb.sdrf.txt	Txt
	E-GEOD-8994.idf.txt	Idf
	E-GEOD-8994.processed.1.zip	Processed
	E-GEOD-8994.processed.2.zip	Processed

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A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis.

Chen Junfeng J Agrawal Vikas V Rattray Magnus M West Marilyn A L MA St Clair Dina A DA Michelmore Richard W RW Coughlan Sean J SJ Meyers Blake C BC

BMC genomics 20071112

<h4>Background</h4>Several high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more recently developed methods based on sequence tag abundances such as the Massively Parallel Signature Sequencing (MPSS) technology. A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors ...[more]

PMID: 17997849

Similar Datasets

Project description:BACKGROUND: Several high-throughput technologies can measure in parallel the abundance of many mRNA transcripts within a sample. These include the widely-used microarray as well as the more recently developed methods based on sequence tag abundances such as the Massively Parallel Signature Sequencing (MPSS) technology. A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. RESULTS: We compared transcript abundance (gene expression) measurement data obtained using Affymetrix and Agilent microarrays with MPSS data. All three technologies were used to analyze the same set of mRNA samples; these samples were extracted from various wild type Arabidopsis thaliana tissues and floral mutants. We calculated correlations and used clustering methodology to compare the normalized expression data and expression ratios across samples and technologies. Abundance expression measurements were more similar between different samples measured by the same technology than between the same sample measured by different technologies. However, when expression ratios were employed, samples measured by different technologies were found to cluster together more frequently than with abundance expression levels.Furthermore, the two microarray technologies were more consistent with each other than with MPSS. We also investigated probe-position effects on Affymetrix data and tag-position effects in MPSS. We found a similar impact on Affymetrix and MPSS measurements, which suggests that these effects were more likely a characteristic of the RNA sample rather than technology-specific biases. CONCLUSION: Comparisons of transcript expression ratios showed greater consistency across platforms than measurements of transcript abundance. In addition, for measurements based on abundances, technology differences can mask the impact of biological differences between samples and tissues.

Project description:We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.