Comparative transcriptome analysis of JAZ4 knock-out plants (jaz4-1) and Col-0 Arabidopsis thaliana plants.

Time point RNAseq analysis of jaz4-1 mutant vs Col-0 reveals dynamic JAZ4 mediated regulatory pathways. Overall design: Arabidopsis thaliana (L. Heyhn.) seeds were sown directly onto soil (SunGro Horticulture Sunshine Mix #1) in tray plugs (3.5 x 3.5 x 5.5 cm) or pots (5 cm3). Plants were kept in growth chamber maintained at 22 degree C, with a 12-hour photoperiod, light intensity of 100 ± 20 µmol/m2/sec, and 60 ± 5% relative humidity. The wild type ecotype Columbia (Col-0, ABRC stock CS60000) and its derivative JAZ4 knockout mutant jaz4-1 (SALK_141628C) were obtained from the Arabidopsis Biological Resource Center (ABRC). Three week old rosette shoots were collected at six-hour increments starting at dawn and spanning 18 hours (ZT 0, 6, 12, and 18). Three biological replicates were sampled, each containing six rosettes that were cut at the hypocotyl region, immediately frozen in liquid nitrogen, and stored at -80oC until the time for tissue processing.