GSM7017306: DAP_bZIP76_deM_SE50; Zea mays; OTHER
DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017).  RNA-seq: RNA extraction was conducted using Trizol (Invitrogen) following the company's recommended procedure. The RNA integrity and concentration were checked on 1.5 % agarose gel and Qubit RNA HS assay, respectively. DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017) except for the following: Approximate 200 ng of DAP-seq gDNA library was added as an input for incubation with each pIX-HALO-TF protein extract. To perform double-size selection of 200-300 bp fragments for each sample, 0.8 volume of Agencout AMPure XP beads (40ul) to 1 volume of sample (50ul) were mixed for 5 minutes and the bead were discarded to remove fragments with size larger than 300 bp. Next, the supernatant (90 ul) contain < 300bp fragments were added to 0.2 volume of Agencout AMPure XP beads (10 ul) and mixed for 15 minutes. Bound DNA was eluted by adding 18 ul UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen). The DNA concentration of DAP-seq libraries was evaluated using Qubit HS dsDNA assay kit, and approximate 5-20 ng/μl final concentration were obtained. Fragment sizes were further examined by agarose gel electrophoresis after six cycles of PCR using 2ul of DAP-seq library in 20 ul total volume with library specific primer pairs. RNA-seq: Samples with sharp rRNA bands were used for RNA-seq library preparation using TruSeq RNA library pre kit v2 (Illumina) following the manufacturer instructions. The RNA libraries (in pools of 9 samples each using Illumina barcodes) were sent to the Genomic Core Facility at Michigan State University for 50 bp single-end sequencing on the Illumina Hiseq 4000. ChIP-seq: All ChIP-seq librares were made using NEBNext Ultra II DNA library Prep kit for Illumina (NEB#7645 S/L, $E7103 S/L). Hiseq4000 were used for all SE50 sequencing.