Auxin and ABA responsiveness in the root or the shoot of dark-grown Arabidopsis thaliana 5 day old seedlings in the aba2-3 or wild-type (Col-O) background

We report differences in the transcriptional responses of the root and the shoot to either auxin or ABA in comparison to mock treatment in dark-grown Arabidopsis thaliana seedlings. By examining the auxin responsiveness in the shoot or the root of a dark-growh ABA biosynthesis mutant, we found that auxin relies on intact ABA biosynthesis in order to regulate aspects of transriptional output. Overall design: All seedlings were first stratified for 2 days at 4 degress celsius and then grown under continious light for 24 hours to initiate germination, which was followed by 4 days in complete darkeness at 22 degrees celsius. At this point, the seedlings were treated with either 10uM IAA, 10uM ABA, or equivalent ethanol for mock for 2 hours using a green safe light for seedling transfer. After 2 hours the seedlings were bisected at the root shoot junction and immediately frozen in liquid nitrogen, which was followed by RNA isolation. In total 10 different genotype/treatment/tissue combinations analyzed and each combination had 3 replicates bringing the total number of samples to 30. The mock treatments of either Col-O or aba2-3 were the controls used.