Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells/Wen et al. reply

Variations in sample labeling or hybridization conditions, for instance, can easily account for the 0.2-0.4 log2 unit differences they observe (Supplementary Fig. 1). [...] the authors did not rule out systematic experimental errors related to the chromatin immunoprecipitation procedure, such as differences in epitope accessibility or locus-dependent variation in the efficacy of chromatin extraction between cell types. Notice that the procedure and cutoff we used in the paper worked remarkably well at detecting locations with differential LOCKs between samples as confirmed by (i) RT-PCR for gene expression, (ii) association with gene expression in tissues and (iii) concordance with replicate experiments (ref. 1, Fig. 1 and Supplementary Fig. 1).\n Kalmar et al. have now proven that ES cells are dynamically heterogeneous at the population level5.