title: RNA-seq of Zea mays: primary root 2-4 cm length
design: Seeds of the maize inbred lines Oh43, W64A and their reciprocal F1-hybrids W64AxOh43 and Oh43xW64A were surface sterilized and germinated in moist germination paper. The primary roots of the seedlings were harvested at a length of 2-4 cm. Samples were harvested in four biological replicates, each sample consists of 10 pooled primary roots resulting in 16 distinct samples (4 genotypes x 4 replicates). The total RNA of pooled root samples was isolated with the RNeasy Plant Mini Kit (Qiagen, Venlo, The Netherlands). RNA quality was assessed via a Bioanalyzer (Agilent RNA 6000 Pico Chip, Agilent Technologies, Santa Clara, USA). For all samples, a RIN ? 9.6 detected. For each of the 16 samples, 20 ng high quality RNA was used for cDNA synthesis and ampli?cation. cDNA synthesis and libraries for Illumina sequencing were constructed according to the protocol of the manufacturer (TruSeq RNA Sample Preparation, Illumina, San Diego CA, USA). For sequencing, each library was indexed by an Illumina TruSeq Adapter. Indexed libraries were pooled on one lanes of a flow cell. Cluster preparation and pair-end read sequencing were performed according to the manufacturer?s instructions (HiSeq 2000, Illumina, San Diego CA, USA).