Suppl dataset 4 RNA isoforms (3 h to 0 h)

RNA isoforms were analyzed using the RNAseq data to gauge the level of alternate RNA splicing. Differential exon usage was computed using a flattened maize gene model file with collapsed exon counting bins. For alternative splicing analysis, the number of reads were counted that overlaped with each of the exon counting bins. To identify exons skipped, each sample was compared to the sample from next immediate time point i.e. 3 h and 6 h, 6 h and 12 h, 12 h and 24 h, etc. Attached data compares time points 3 h to 0 h. Other time point comparisons are available on request.