Additional file 9.

Chromatin profiles of expression-matched CpG and non-CpG promoter genes in IMR90 cells. Note that the CD4+ T-cell chromatin profiles shown in the main paper and the IMR90 chromatin datasets shown here were generated with different chromatin immunoprecipitation protocols. In the case of CD4+ T cells, nucleosomes were isolated by micrococcal nuclease digestion before immunoprecipitation. In the case of IMR90 cells, chromatin was sonicated before immunoprecipitation. These experimental differences may account for some of the differences in the CD4+ T-cell chromatin profiles and the IMR90 chromatin profiles. The GEO file accession numbers for the datasets used here are GSE2672 (a), GSM521890 (b), GSM521915 (c), GSM521904 (d), GSM752986 (e), GSM521899 (f), GSM521895 (g), GSM521866 (h), GSM521881 (i), GSM521885 (j), GSM469975 (k). Promoters are annotated according to UCSC downloaded CpG islands [5].

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Vavouri and Lehner Genome Biology 2012 13:R110   doi:10.1186/gb-2012-13-11-r110