The raw contigs FASTA file, the GTF annotations and the peptide sequences were downloaded from:ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/

The hard-masked FASTA file was produced by Perl conversion of the soft-masked sequence from RefSeq with the following:

perl -lne 'if(!/^>/){ s/[a-z]/N/g } print' Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna.toplevel.fa > \
    Arabidopsis_thaliana.Columbia.GCF_000001735.3_TAIR10.NCBIRefseq.dna_rm.genome.fa

The rest of files were produced by RSAT-Tools to install this genome.