Zea mays ssp. mays L. CML228 seedling shoot RNA-Seq
10 kernels of each line were germinated in germination paper and placed in a tall plastic beaker filled with approximately 3 inch of tap water. They were covered with "Cling-wrap" to avoid evaporation and to maintain a water-saturated environment. The plastic beakers were placed in a dark 28C incubator, for approximately 4-5 days, until shoots emerged from the germination paper. 2-3” of the shoot and root were cut and frozen in liquid nitrogen for homogenization and extraction.  All RNA extractions were conducted using the Qiagen RNeasy kit cat# 74904 (50), according to Qiagen's protocol. Total RNA was eluted twice with 30 ul RNase-free water. The indexed RNA-Seq libraries were prepared using the Illumina protocol outlined in "TruSeq RNA Sample Preparation Guide" (Part# 15008136 Rev. A November 2010). The indexed libraries from one inbred/line were combined and seeded onto one lane of the flowcell. The libraries were sequenced using 110 cycles of chemistry and imaging, resulting in paired-end (PE) sequencing reads with length of 2 x 101 bp.