Spot blotch is a disease of barley caused by the fungus Bipolaris sorokiniana (teleomorph: Cochliobolus sativus). A Minnesota (USA) malting cultivar, Morex, is durably resistant to this pathogen. The resistance is known to by conferred by a suite of quantitative trait loci known as the Midwest Six-rowed Durable Resistance Haplotype (MSDRH). We used gamma radiation to induce susceptibility in Morex. The mutant (MUT 14-40) is susceptible to spot blotch at the seedling stage and displays very large necrotic lesions at the adult plant stage. The adult-onset necrosis will not be discussed further here because it takes place at a later growth stage. The fungus switches its lifestyle from that of a biotroph to that of a necrotroph around 24 hours after infection. Therefore, we are interested in the early infection period. We conducted an experiment to study the transcriptomic response at the early infection stage (12, 24, and 36 hours after inoculation). The experimental design was completely randomized and included resistant barley accessions (NDB112 and Bowman) as well as the susceptible barley line ND5883 as checks. These are standard differentials for checking expected reaction types, although RNA was not collected from these genotypes since they were not the focus of the experiment. The data presented here are from an RNA-seq time course experiment (at 12, 24, and 36 hours after inoculation and mock (water) inoculation). The genotypes are the wild-type Morex (WT) and the Morex Mutant (MUT 14-40). Treatments are either inoculated or mock-inoculated (water treated). There were three (3) replicates. Isolate ND85F (commonly used to represent pathotype 1 of the pathogen) was used for the inoculated set. Pathotype 1 is avirulent on NDB112 and Bowman, but is virulent on ND5883. The controls reacted as expected. The RNA-seq expression matrix is in the file 170309_morex_and_mut_rnaseq_expression_data.csv). The qPCR data (in file 170424_morex_and_mut_qpcr_raw_data.csv) are also provided for select genes chosen as a validation approach. The expression of two genes (HORVU3Hr1G019920 and HORVU5Hr1G120850) were completely abolished.