H3K27me3 Profiling in Brassica rapa

The dataset of the genome-wide H3K27me3 profile (NCBI SRA number: PRJNA542357) in leaf and inflorescence tissues of R-o-18 inbred line (B. rapa ssp trilocularis) was downloaded. The reference genome of B. rapa was also downloaded from Ensembl Plants database (https://plants.ensembl.org/). The downloaded raw fastq files of H3K27me3 were initially quality-checked using the FastQC program (Andrews, 2010 ). On the basis of FastQC result, low-quality reads were trimmed and filtered using Trimmomatic (v0.36) (Bolger et al., 2014 (link)), and the filtered fastq files were used for mapping to B. rapa genome by using bowtie2 (Langmead and Salzberg, 2012 (link)). SAMtools (Li et al., 2009 (link)) were used to convert SAM files to BAM files. Then, duplicated reads were removed by Picard MarkDuplicates (v2.18.2.0; biotools:picard_tools; RRID : SCR_006525). Deduplicated reads were then used for peak calling on pooled replicates by using MACS2 (v2.1.1) for comparison between input DNA and ChIP samples. The distribution of H3K27me3 enrichment was visualized using the IGV (Thorvaldsdóttir et al., 2013 (link)).