P-GSE43142-3 - P-GSE43142-3
Raw sequencing reads from all libraries were mapped to the reference genome of the maize inbred line B73 (version 2; ZmB73_RefGen_v2) (
) (Schnable et al., 2009) using Bowtie software (Langmead et al., 2009). Sequencing reads from mRNA-seq were also mapped to Mo17 whole-genome shotgun sequences (
) using the same software. For the data of mRNAs, histone modifications and DNA methylation, up to two mismatches per read were allowed during the alignment procedure. For small RNA data, the 3’ adapter sequences were removed by a custom Perl script before alignment, and adapter-trimmed small RNA reads which were perfectly matched to the reference genome were retained. Small RNA sequencing reads matched to tRNAs, rRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) were also excluded from further analysis. For all sequencing data, the reads mapped equally well to multiple locations in the genome without mismatch or with identical mismatches were assigned to one position at random. Genome_build: B73 RefGen_v2 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples, read counts for ChIP and McrBC seq peaks, and read counts for small RNA seq clusters.