ChIP-seq analyses
ChIP-seq libraries were obtained from the NCBI Sequence Read Archive (SRA) (https://www.ncbi.nlm.nih.gov/sra). Raw reads were processed for quality control using the FastQC v0.12.1 program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapter sequences were trimmed using Trim Galore (v.0.5.0) with a minimum base quality threshold of 20. Clean reads were aligned to the corresponding genome using Bowtie v2 2.3.5.1 (Langmead and Salzberg, 2012) with default parameters. Reads aligned to chloroplast or mitochondrial sequences were subsequently filtered out. Significant peaks were identified using MACS2 (Zhang et al., 2008) with the parameters ‘‘--nomodel -f AUTO --keep-dup 1 -q 0.05’’.

Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., et al. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137.