RNA-Seq mapping enabled quantitative analysis of gene expression differences between normal and ded1-ref in Zea mays (Maize)

The goals of this study are to compare NGS-derived transcriptomes (RNA-Seq) derived from ded1-ref mutant and normal maize endosperm tissue. Homozygous ded1-ref mutants exhibit a seed defect. Maize Ded1 encodes a transcription factor. This study characterizes DEGs between ded1-ref and normal endosperm and serves to identify direct target genes together with DAP-seq data. Overall design: Endosperm mRNA profiles from 12 days after pollination (DAP) normal and ded1-ref kernels in the Zea mays W22 background were generated by deep RNA-Seq. Total RNA was prepared for 4 biological replicates of paired ded1-ref and normal sibling pools. 2x100bp PE sequencing performed on an Illumina HiSeq2000.