A transcriptome sequence dataset characterizing eggs, nymphs and adults of Oxycarenus hyalinipennis, the cotton seed bug

is an agricultural pest that has recently been detected in the United States and has the potential to cause extensive economic damage to the cotton production industry. Currently, there are no transcriptomic resources for this species. The data reported here will serve to help guide future efforts to create additional reference resources as well as facilitate the development of population control strategies. These data could also be of use towards identifying protein coding genes in a cotton seed bug genome assembly. A total of 13,384 differentially expressed genes was identified, which collectively encoded 40,871 distinct transcripts, of which 18,842 could be annotated with a reference protein in the NCBI NR database, 13,233 with Pfam protein families and 8,089 with GO Gene Ontology terms. These transcripts could, for example, be targeted for future functional genomics work.