Suppl dataset 3 ATACseq

ATACseq analysis was conducted in triplicate to identify changes in chromatin “openness” or accessibility in response to ER stress. Maize B73 seedlings were treated with 5 g ml-1 TM for 0, 6 and 12 h. Nuclei were isolated from root samples and incubated with Tn5 transposase to tag DNA fragments in regions of open chromatin. The tagged DNA was PCR amplified with primers directed against the Tn5 inserts and used to construct a cDNA library, which was subject to DNA sequencing. Short read sequences were aligned to the maize genome version 4, and peaks were called for each replicate at every time point. Differential peak scores representing changes in promoter openness in the 500 or 5000 bp upstream region for each gene for 6 h vs 0 h and 12 h vs 0 h were then calculated. Tab 1: from the start of transcription to 500 bp upstream. Tab 2: from the start of transcription to 5000 bp upstream.