title: ChIP-Seq of Panicum hallii: plant leaf tissues
design: We followed the main steps of ChIP sequencing by ZymoSpin ChIP Kit protocol with some modifications. ChIP-Seq service was performed by Zymo Research Corporation. Briefly, plant tissue was formaldehyde cross-linked for 10 min at room temperature, and chromatin was prepared using the Zymo-Spin ChIP kit (Zymo Research Corp., Irvine, CA) following a modified protocol for isolation of plant chromatin. Sonication was performed at high power setting for 40 cycles (30 s on, 30 s off) using a Bioruptor Plus (Diagenode Inc., Denville, NJ), yielding fragment size range of 200-700 bp. The ChIP assay was performed using 12 g of chromatin and 10 l of anti-PRMT1 (Abcam ab376). Anti-IgG (Millipore, PP64B; Lot 2565474) at a concentration included as a negative control. ChIP DNA was purified using the ChIP DNA Clean and Concentrator (Zymo Research, Irvine, CA). ChIP-Seq libraries were prepared and sequenced on a MiSeq sequencer (Illumina, San Diego, CA). ChIP-Seq reads were aligned to the Panicum hallii reference genome (version 2) by Bowtie with at most 2 mismatches. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication. BIGWIG files were generated from the coverage for visualization purposes. MACS2 was used to identify peaks at q-value cutoff 0.05 and a broad cutoff of 0.1.