Temporal comparison of leaf transcriptomes between early-flowering Arabidopsis thaliana atx1/atx3/atx4 triple mutants and vegetative WT Col-0 plants of the same age.

atx1/atx3/atx4 triple mutants display significantly early flowering and early leaf senescence phenotypes. RNA-seq was used to identify gene expression changes occuring at the time of bolting, independent of leaf age. Overall design: Two homozygous atx1/atx3/atx4 triple T-DNA insertion mutants were isolated (TM1 and TM2). Both have the same T-DNA mutant alleles but come from different crosses so they may contain different background mutations. atx triple mutants display significant early flowering and significant early leaf senescence phenotypes. Previous phenotype analyses show that early leaf senescence was detected at day 33 in the triple mutants. RNA-seq was used to identify gene expression changes occurring at the time of bolting that might be promoting the onset of leaf senescence, thus coupling the early flowering phenotype to the early leaf senescence phenotype (see "Timeseries Design Infographic"). Triple Mutants bolting at the peak of triple mutant bolting (Days 24 and 25, see "Peak of Triple Mutant Bolting Info" for details) were pooled and then 1/4th of these bolting plants were harvested. Plants were then randomly selected for harvesting from this pool in two day increments, three times. Thus, harvesting days were 25, 27, 29, and 31 days after stratification. This strategy was used to ensure the TM plants harvested at each time point were developmentally similar. The sixth leaf to emerge was harvested from each plant. Three replicates were generated per line, per time point (4 time points), totaling to 12 cDNA libraries per genotype. The 36 cDNA libraries were prepared using the BrAD-seq protocol and were then sequenced at the University of California, Irvine Genome High-throughput Facility. "Peak of Triple Mutant Bolting Info", "Timeseries Design Infographic", "BrAD-seq Info". These images were included to help understand the experimental design.