During the Stratosphere-Troposphere Analyses of Regional Transport 2008 Experiment (START08) the NCAR/NSF Gulfstream V aircraft encountered high concentrations of NO and NOy in the upper troposphere downwind of a squall line in north Texas, suggesting either convective transport of polluted boundary layer air to the upper troposphere or lightning induced production of nitrogen oxides in the convection. These hypotheses are tested by computing three-dimensional back-trajectories using winds from a high-resolution simulation of the event with the Weather Research and Forecasting (WRF) Model. The WRF model simulation reproduces the storm structure and evolution with good fidelity. The back trajectories reveal two distinct layers of out flow air from different mesoscale convective systems (MCSs). Most air in the upper layer is transported northward from an MCS in south Texas, while the lower layer is from both the squall line and the southern MCS. The predicted concentrations of CO and NOy using a simple chemical model show that the back trajectories capture the vertical profile of CO in the lower layer and of NOy at the bottom and top of the lower layer. The enhanced NOy could be explained by lightning during the time the out flow air was ascending in the convective updrafts using data from the National Lightning Detection Network (NLDN). In the upper layer, the large discrepancy of NOy between observation and model seems to be caused by the lack of lightning source and a notable underestimate of the vertical transport to the very top of the troposphere by the MCS.