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Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

Eun-Ang Raiber1†, Dario Beraldi1,2†, Gabriella Ficz3, Heather E Burgess3,4, Miguel R Branco3,4, Pierre Murat1, David Oxley5, Michael J Booth1, Wolf Reik3,4*† and Shankar Balasubramanian1,2,6*

1 Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

2 Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson way, Cambridge, CB2 0RE, UK

3 Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

4 Centre for Trophoblast Research, University of Cambridge, Physiology Building, Downing Street, Cambridge CB2 3EG, UK

5 Proteomics Research Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

6 School of Clinical Medicine, The University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0SP, UK

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Genome Biology 2012, 13:R69 doi:10.1186/gb-2012-13-8-r69

Published: 17 August 2012

Additional files

Additional file 1:

Supplementary figures and tables.

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Open Data

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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