1. Oligos used in the production of the microarrays are from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0, while the custom made oligos were produced by Operon (Alameda, CA, USA) or MWG (Ebersberg, Germany). Information about the AROS probes is available at: http://omad.operon.com/arabidopsis/ 2. Oligos are arrayed in Genetix X6004 384 well plates with V-shaped bottom. Each well contain 600 pmol 70 mer oligo 3. Oligos were resuspended in 16 µl Milli-Q-filtered DNase free water and 8 µl from each well were transfered to new set of Genetix X6004 384 well plates using a Tecan Genesis RSP 200 liquid handling workstation. 4. 8 µl DMSO were added to each well giving a final oligo consentration of ~20 µM and 50% DMSO. 5. The plates were sealed with ABgene Adhesive PCR Foil seals and centrifuged at 1000 rpm in a Sorvall RT6000B centrifuge. The plates were stored at -20C. 6. The plates were thawed and placed on a rotary shaker for 12 hour before printing of oligos. 7. The oligos were printed on amino silane coated UltraGaps slides (Corning, NY, USA) using a BioRobotics MicroGrid II robot (Genomic Solutions, MI, USA). 8. After printing the micorarray slides were exposed for UV light in a Stratalinker 2400 UV crosslinker (Stratagene), at 800 milijoules/cm2. 9. Microarray slides were stored under low humidity conditions and not exposed to light.
Systems Biology approach to identify transcriptome reprogramming in Arabidopsis thaliana during insect and bacterial attack (Pseudomonas syringae)
Data table header descriptions
ID
Unique spot identifier
Block
Block (1-48)
Column
Column (1-26)
Row
Row (1-27)
Locus ID
Oligo ID
Custom oligo IDs and oligo IDs from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0 (http://omad.operon.com/arabidopsis/)
Gene_Desc
Gene description (TAIR9)
SEQUENCE
Probe sequence information from custom made oligos.
ATPRX Q (Thioredoxin superfamily protein); encodes periredoxin Q which decomposes peroxides and plays a role in the protection of the photosynthetic apparatus
WPP2 (WPP domain protein 2); WPP family members contains an NE targeting domain. This domain, called the WPP domain after a highly conserved Trp-Pro-Pro motif, is necessary for NE targeting of WPP1. RNAi suppression of WPP2 resulted in reduced mitotic activity.
CAD2 (CADMIUM SENSITIVE 2); Encodes the enzyme glutamate-cysteine ligase catalyzing the first, and rate-limiting, step of glutathione biosynthesis. Required for cell proliferation at the root tip. Involved in susceptibility to the bacterial pathogen Pseudomonas syringae. Mutants are phytoalexin defective.
ATEXO70E1 (exocyst subunit exo70 family protein E1); A member of EXO70 gene family, putative exocyst subunits, conserved in land plants. Arabidopsis thaliana contains 23 putative EXO70 genes, which can be classified into eight clusters on the phylogenetic tree.
ATNADP-ME4 (Arabidopsis thaliana NADP-malic enzyme 4); The malic enzyme (EC 1.1.1.40) encoded by AtNADP-ME4 is localized to chloroplasts. The gene is expressed throughout the whole plant and during embryogenesis and germination. A possible involvement in the fatty acid biosynthesis has been proposed.
Less...
More...