Additional file 2.
Genomic coordinates of 5fC-, 5hmC- and 5mC-enriched regions in wild type and knockdown. These bed files report the genomic positions of the regions enriched in 5fC, 5hmC and 5mC. The reported regions are the intersection of the enrichment between two replicates. For each region, the position of the nearest CGI is also shown (where multiple CGIs have the same distance, only the first one is reported). The columns in these files are: 1) chrom (chromosome); 2) start (enriched region start); 3) end (enriched region end); 4) name (ID for enriched region); 5, value (unused column); 6) strand (strand (always +)); 7) cgi_start (nearest CGI start); 8, cgi_end (nearest CGI end); 9) cgi_id (CGI ID (from UCSC genome browser table cpgIslandExt.bed)); 10) cgi_dist (distance of CGI from enriched region (0 if overlapping)). The files in the zipped directory are: fc.enriched.cgi.bed (regions enriched in 5fC in wild-type); fc_sirna_ctrl.enriched.cgi.bed (regions enriched in 5fC in siRNA control); fc_tdg_vs_ctrl.enriched.cgi.bed (regions enriched in 5fC in TDG KD relative to siRNA control); hmc.enriched.cgi.bed (regions enriched in 5hmC wild-type); mc.enriched.cgi.bed (regions enriched in mC wild type).
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Raiber et al. Genome Biology 2012 13:R69 doi:10.1186/gb-2012-13-8-r69