|
| Status |
Public on Jan 08, 2007 |
| Title |
Comparison of CATMA, Affymetrix and Agilent arrays |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
|
| Summary |
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
Keywords: unknown_experiment_design_type
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| |
|
| Overall design |
8 samples were used in this experiment
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| |
|
| Contributor(s) |
Beynon J, Townsend H, Emmerson Z, Schildknecht B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 01, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Nottingham Arabidopsis Stock Centre (NASC) |
| E-mail(s) |
affy@arabidopsis.info
|
| Phone |
+44 (0)115 951 3237
|
| Fax |
+44 (0)115 951 3297
|
| URL |
http://arabidopsis.info/
|
| Organization name |
Nottingham Arabidopsis Stock Centre (NASC)
|
| Department |
School of Biosciences, University of Nottingham
|
| Street address |
Sutton Bonington Campus
|
| City |
Loughborough |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
|
| Samples (8)
|
| GSM133861 |
Beynon_1-4-cat-SpikeMix4_Rep1_ATH1 |
| GSM133862 |
Beynon_1-5-cat-SpikeMix5_Rep1_ATH1 |
| GSM133863 |
Beynon_1-6-cat-SpikeMix6_Rep1_ATH1 |
| GSM133864 |
Beynon_1-7-cat-SpikeMix7_Rep1_ATH1 |
| GSM133865 |
Beynon_1-8-cat-ReferenceMix_Rep1_ATH1 |
|
| Relations |
| BioProject |
PRJNA97051 |
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