Juglans regia Transcriptome or Gene expression

We previously developed a novel crown gall resistance strategy for walnut trees. RNAi is used to silence two oncogenes of Agrobacterium tumefaciens (Escobar et al., 2002 http://www.sciencedirect.com/science/article/pii/S0168945202001644 ). In the current experiment, wild-type Chandler walnut scions have been grafted onto either wild-type Paradox walnut rootstock (control) or Paradox rootstock containing the RNAi construct (transgenic), with three biological replicates of each condition (control and transgenic), and three samples from each biological replicate: “scion” (above the graft union), “rootstock” (below the graft union), and “union” (through the graft union). These samples are comprised of mostly phloem cells (tissue exterior to the vascular cambium). In addition, mature nuts were collected from two of the replicates for each condition. The kernel and pellicle were excised separately. Small RNA was isolated from each of these 24 samples. Illumina TruSeq small RNA libraries were constructed for each sample. Twelve libraries were sequenced on each of two HiSeq lanes.