GSE132167
Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1
MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods:  mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings  were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change =2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation. Overall design: RNA-seq and Sequence Capture Bisulfite-seq was preformed on homozgyous Mop1 wildtype and mop1-1 mutant V3 seedling shoots with and without exogenous 50 µM ABA treatment  for 7 (SeqCap) or 8 hours (RNA-seq).