normalized_cufflinks_<species>_expression.txt: these files contain the expression value of all annotated genes and retrocopies from each RNA-seq sample. Expression values are measured in FPKM using Cufflinks.

Mouse_H3K4me1_peaks_<organ>.bed: these files contain the genomic coordinates of H3K4me1 peaks in mouse organs.

Mouse_H3K4me3_peaks_<organ>.bed: these files contain the genomic coordinates of H3K4me3 peaks in mouse organs.

Mouse_H3K27ac_peaks_<organ>.bed: these files contain the genomic coordinates of H3K27ac peaks in mouse organs.

Mouse_<ChIP-seq_experiment>_mean_coverage_at_rat_retro_integration_loci.txt: these files contain the mean read coverage of each mouse ChIP-seq experiment extracted from mouse regions corresponding to the integration sites of rat-specific retrocopies. Each files contains the genomic locus of the mouse regions, the name of the corresponding rat retrocopy integrated in the orthologous region, and the mean ChIP-seq read coverage. When two genomic locations corresponding to two distinct integration sites overlap, the two loci are merged and the corresponding retrocopies indicated (separated by a semicolon).

Mouse_<ChIP-seq_experiment>_read_count_at_rat_retro_integration_loci.txt: these files contain the read count over each mouse ChIP-seq experiment extracted from mouse regions corresponding to the integration sites of rat-specific retrocopies. Each files contains the genomic locus of the mouse regions, the name of the corresponding rat retrocopy integrated in the orthologous region, and the read count. When two genomic locations corresponding to two distinct integration sites overlap, the two loci are merged and the corresponding retrocopies indicated (separated by a semicolon).

