Zea mays
For this transcriptome study, seedling of the maize inbred line SCML0849 ans ZnC442 were surface sterilized and germinated in moist germination paper. About 7-day old uniform seedlings were transferred to hydroponics system cultured by high nitrate (4 mM) nutrient solution. The seedlings were cultured in this system until 5 leaf stage then the roots were by CK, low nitrate deficiency (0 mM) or drought (15% PEG) solution. After 48 h of incubation, leaf  samples were dissected then stored in liguid nitrogen. Experiments were performed in three biological replicates each sample consisting of 10 plants resulting in 48 distinct samples (leaf sample3 treatments x 4 genotypes x 3 replicates). The total RNA of captured cells was isolated with trizol agent (Invitrogen). RNA quality was assessed via a Bioanalyzer (Agilent RNA 6000 Nano Chip, Agilent Technologies, Santa Clara, USA). For all samples, a RIN ≥ 6.5 detected. cDNA 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 in which no adapter was used more than twice. Indexed libraries were loaded onto a flow cell following an incomplete block design with four pooled libraries per lane. Cluster preparation and pair-end read sequencing were performed according to the manufacturer's instructions (HiSeq 4018, Illumina, San Diego CA, USA).