Primary leaves of three-weeks-old soybean plants cultivar Williams 82 were inoculated with a Mississippi isolate of Phakopsora pachyrhizi (MS06-1). The first trifoliate leaves were collected 15 seconds after inoculation, used as a time-zero, and 10 days after inoculation. RNA was isolated and extracted from the infected leaves and cDNA libraries were constructed. cDNA was then sequenced on an Illumina platform. Reads in this study did not map to the Glycine max genome.