GSE124245
RNA-Seq from zmknl1 and WT kernels at 14 DAP (day after pollination) with each two independent biological replicates
To further understand the basis of the phenotypic defects in the zmknl1 mutant, we performed RNA-Seq from zmknl1 and WT kernels at 14 DAP with each two independent biological replicates. Totally 555 significantly differentially expressed genes (DEGs) were identified according to these RNA-Seq data (q-value <0.05, log2(fold change) >= 1.5), with 317 down- and 238 up-regulated genes. Overall design: Two independent biological replicates from different ears were used in the study. The cDNA libraries were constructed following Illumina standard protocols and sequenced with Illumina HiSeq 2500 by Berry Genomics Co. Ltd, China. Sequenced reads were trimmed using Trimmomatic (version: 0.36), then mapped to B73 RefGen_v3.31 using hisat2 (version: 2.0.1-beta). Htseq-count was used to count reads of all the annotated genes. Significant DEGs were identified using DESeq2 package as those with threshold (q < 0.05,log2(fold change) > 1.5).