| Experiment: | 94 |
| Title: | Comparison of CATMA, Affymetrix and Agilent arrays |
| Date: | 2004-08-11 |
| 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. |
| ftp Link: | ftp Link |
| Slide ID | Slide Name | Genetic Background | Tissue | Stock Code | Cel File |
|---|
| Beynon_1-1-cat-SpikeMix1_Rep1_ATH1 | 862 | | whole shoot | N3176 | JB001_ATH1_A1-Beyno-cat.CEL |
| Treatment: Spike Mix 1 |
| Beynon_1-2-cat-SpikeMix2_Rep1_ATH1 | 863 | | whole shoot | N3176 | JB001_ATH1_A2-Beyno-cat.CEL |
| Treatment: Spike Mix 2 |
| Beynon_1-3-cat-SpikeMix3_Rep1_ATH1 | 864 | | whole shoot | N3176 | JB001_ATH1_A3-Beyno-cat.CEL |
| Treatment: Spike Mix 3 |
| Beynon_1-4-cat-SpikeMix4_Rep1_ATH1 | 865 | | whole shoot | N3176 | JB001_ATH1_A4-Beyno-cat.CEL |
| Treatment: Spike Mix 4 |
| Beynon_1-5-cat-SpikeMix5_Rep1_ATH1 | 866 | | whole shoot | N3176 | JB001_ATH1_A5-Beyno-cat.CEL |
| Treatment: Spike Mix 5 |
| Beynon_1-6-cat-SpikeMix6_Rep1_ATH1 | 867 | | whole shoot | N3176 | JB001_ATH1_A6-Beyno-cat.CEL |
| Treatment: Spike Mix 6 |
| Beynon_1-7-cat-SpikeMix7_Rep1_ATH1 | 868 | | whole shoot | N3176 | JB001_ATH1_A7-Beyno-cat_repeat.CEL |
| Treatment: Spike Mix 7 |
| Beynon_1-8-cat-ReferenceMix_Rep1_ATH1 | 869 | | whole shoot | N3176 | JB001_ATH1_A8-Beyno-cat.CEL |
| Treatment: Reference Spike Mix |
NASCArrays Information at The BAR
Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed
from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the
experiment number. To download the CEL files, please click on the ftp link.