Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation

To find novel factors in early root system architecture responses to nitrate conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient nitrate conditions. Overall design: Col-0 seeds were surface sterilized and plated on mesh on 1mM KNO3 media and stratified for 2 days at 4°C . Plates were then placed vertically and grown in 22°C in 16 hour days/8 hour nights. 7 day old plants were transferred either to new 1mM or 10mM KNO3 plants at two hours post-dawn in the growth chamber. Per biological replicate, two plates per time point were transferred then combined. Root tissue was then harvested and flash frozen in liquid N2 at 0 min (mesh was picked up and placed down on the same plate to account for mechanical responses to transfer), 15 min, 45 min, 90 min, and 180 min.