Transcriptomics,Multiomics

Dataset Information

3

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

Dataset's files

Source:
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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Publications

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]

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