Figure 1

Microarray design and UV-B irradiation apparatus. (a) Microarray hybridization design with direct comparisons to measure UV-B effects on signaling initiation from irradiated to shielded tissues: 1) controls, 2) dosage comparison for leaves, 3) dosage comparison for ears, 4) time course comparison for leaves, and 5) time course comparison for ears. The dosage treatments were all done at a standard time of 4 h irradiation, and all time course treatments had two leaves exposed above the PE. Each arrow represents a pair of samples hybridized on one array; in every case there is one cy3-labeled sample compared to one cy5-labeled sample. For each sample type there were four biological replicates, generating at least four hybridization comparisons, except where noted. Dotted blue arrows signify a "virtual" replication in which the comparison of the same samples occurred elsewhere in the design. (b) UV-B-irradiation apparatus for selective leaf irradiation. Irradiated leaves were threaded through slits in the PE plastic to permit UV-B irradiation and collected after irradiation; mature shielded leaf samples were collected immediately below the cut-off filter. Immature ears were dissected from encasing husks leaves after treatments. For the control plants, the PE filter plastic was removed from the apparatus. No UV-B irradiation (NI) control plants were sampled without moving under the apparatus and thus did not receive UV-B; whole irradiated plants (WPI) received UV-B without any PE shielding. See Materials and methods for details of the tissue sampling protocol.