E-GEOD-5739 - Transcription profiling of Arabidopsis to compare of CATMA, Affymetrix and Agilent arrays

Status
Submitted on 1 September 2006, released on 14 June 2008, last updated on 10 June 2011
Organism
Arabidopsis thaliana
Samples (8)
Array (1)
Protocols (10)
Description
Transcript profiling is crucial to study biological systems and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the characteristics of the CATMA microarray designed for Arabidopsis thaliana transcriptome analysis, and compared it with two commercial platforms from Agilent and Affymetrix. The CATMA array consists of gene-specific sequence tags of 150 to 500 base pairs, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (TIGR release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled target derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. A total of fourteen cDNA clones were thus selected and used as templates to synthesize bona fide polyadenylated spike RNAs. Each spike RNA was calibrated then mixed in equal amount with one of the other spike RNAs to obtain seven pairs at equal concentration. These seven spike RNA pairs were then combined systematically to construct seven complex spike mixes in a design similar to an ordered Latin square, each mix containing six of the seven spike pairs in staggered concentrations covering five logs. To prevent loss of spike RNA through adsorption to the plastic ware, the spike mixes were prepared in 0.5 µg/µl Col RNA, resulting in a range of concentration from 0.1 to 10,000 copies per cellular equivalent (cpc), assuming that the total RNA contained 1% polyadenalated mRNA and that a cell contained on average 300,000 transcripts. These seven RNA samples included equal amounts of combined spike RNA . To convert the spike hybridization signals to ratios, an eighth sample was prepared, called the reference sample, consisting of the base Col RNA completed with all spike RNAs at a concentration of 100 cpc. The results from the eight experiments using the Affymetrix gene chips (ATH1) are available for analysis or download from this site. Experimenter name = Jim Beynon; Experimenter phone = 01798 470382; Experimenter fax = 01789 470552; Experimenter department = Horticulture Research International; Experimenter institute = Warwick University; Experimenter address = Horticulture Research International; Experimenter address = Wellesbourne; Experimenter address = Warwick; Experimenter zip/postal_code = CV34 6QJ; Experimenter country = UK Experiment Overall Design: 8 samples were used in this experiment
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-5739.idf.txt
Sample and data relationshipE-GEOD-5739.sdrf.txt
Raw data (1)E-GEOD-5739.raw.1.zip
Processed data (1)E-GEOD-5739.processed.1.zip
Array designA-AFFY-2.adf.txt
R ExpressionSetE-GEOD-5739.eSet.r
Links