Transcripts of VQL-2  kernel  grown in optimum soil zinc
In this study, we aimed to present the complete zinc responsive transcriptomes of developing kernel of maize. We generated high-quality reads for 4 different samples  using Illumina HiSeq 2000 sequencing  platform. The transcriptome dynamics was studied by comparison of gene expression. For this,   we used two maize inbred namely VQL-2 and CM-145 which are  the contrasting for high and low kernel zinc-containing maize inbreds, respectively, the former one being an isogenic line of the latter. Further, they were grown  in the low zinc containing soil  as well as optimum zinc containing soil. Ten days-old-cob were harvested,    opened aseptically under laminar flow and kernels were collected carefully with forceps.  ). Equal  amounts of total RNA from three biological replicates  were pooled for all the 4 samples before  library preparation. They were i) VQL-2 kernel grown under low soil zinc   ii) VQL-2 kernel grown under optimum  soil zinc, iii) CM-145 kernel  grown under low soil zinc,   iv) CM-145 kernel  grown under high soil zinc.  Sequencing of all the 4 samples  was performed by the commercial service provider using an Illumina HiSeq 2000 to generate 150 base long paired-end reads. Library preparation was performed following Illumina TruSeq RNA library protocol outlined in “TruSeq RNA Sample Preparation Guide” (Part # 15008136). The raw data  obtained were filtered through the standard Illumina pipeline.  Finally, the filtered reads were mapped to maize  transcripts and FPKM was calculated for each transcript in all the samples to measure their gene expression. Differential expression analysis was performed using Cuffdiff. software. The genes showing differential expression under various stress conditions were identified.