Trees sampled for RNA preparation were all part of the U.S. Forest Service Northern Research Station’s American beech breeding program in Delaware, OH. Tissues were sampled in the summer of 2009 from selected trees growing in naturally forested areas, grafted ramets of parent trees, and seedling progeny. The selected trees, or grafted ramets of the selected trees, were previously tested for beech scale resistance using an artificial infestation procedure . To maximize genetic diversity, five resistant and five susceptible trees originating from a diverse geographic range, that included New Brunswick (Canada), Maine (USA), the lower peninsula of Michigan (USA), the upper peninsula of Michigan (USA), Pennsylvania (USA), and both northern and southern Ohio (USA) were selected for RNA sequencing and SNP discovery. Outer bark tissues including periderm, vascular cambium, and phloem, were harvested using grafting knives sterilized with liquid ethanol and were immediately frozen in a dry ice ethanol bath before transfer to a − 80 °C freezer until shipping overnight to the Schatz Center at Pennsylvania State University in a dry nitrogen shipper to prevent thawing.