This is a total RNA-seq data set of two inbred strains of maize, B73 and Mo17, extracted from experiment E-GEOD-39232 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39232/). E-GEOD-39232 is a larger study which also studied the expression of small RNAs and genome-wide cytosine methylation pattern in the two strains using high-throughput sequencing methods. For total RNA-seq, three biological replicates were used per strain. E-GEOD-39232 was originally submitted to NCBI Gene Expression Omnibus under accession number GSE39232 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE39232) and later imported to ArrayExpress as E-GEOD-39232.