Nature 502, 65–70 (2013); doi:10.1038/nature12587
In this Article, the reduced representation bisulphite sequencing (RRBS) data obtained and analysed were not initially uploaded to the Gene Expression Omnibus (GEO) record, but can now be found under accession number GSE64115, within the GSE49767 super series. Furthermore, gene expression data for two samples (Mbd3+/+ embryonic stem cells and Mbd3+/+ mouse embryonic fibroblasts (MEFs) after 8 days on doxycycline (dox)) were generated previously by our group1 and deposited in the GEO under accession numbers GSM874650 and GSM874654. Further analysis of this data set was included in Figs 3a, 5c and Extended Data Fig. 8a, c of this Article. Also, in Fig. 5c and Extended Data Fig 8c of this Article, the ‘Mbd3+/+ MEF + 8 day dox’ sample was inadvertently mislabelled as ‘Mbd3+/+ MEF + 11 day dox’. This change does not influence the conclusions of the manuscript.
In addition, further details on the experimental settings used to generate the data in the GSE49766 series reported in this Article (under the GSE49767 super series) have been added to the GEO website. It now states that in Fig. 3a and Extended Data Figs 5 and 8, out of 20 independent clonal series generated in our study carrying either the GOF18 ΔPE-Oct4-GFP transgenic reporter (Addgene plasmid 52382) or the complete GOF18 Oct4-GFP transgenic reporter (Addgene plasmid 60527), the clonal series selected for genomic analysis included an Mbd3+/+ clone that carries the GOF18 ΔPE-Oct4-GFP transgenic reporter, and Mbd3flox/− and Mbd3−/− cells that carry the GOF18 Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements). These reporters can be identified when analysing the Oct4 locus in genomic DNA input datasets. As we do not use Oct4–GFP or any other selection for sorting cells before conducting genomic experiments, the difference in transgene reporters would not influence the interpretation of our genomic analysis data in any way. In these genomics studies, the endogenous Nanog and Oct4 loci are not manipulated and are identical between all cell lines because the Oct4–GFP reporters were introduced via random transgenesis and validated for specificity. Notably, for the mouse induced pluripotent stem (iPS) cell efficiency results presented in our Article (for example, in Figs 1 and 2 and Supplementary Videos 1–4), cell lines carried the matched Nanog–GFP knock-in reporter or Oct4–GFP transgenic reporter (containing both distal and proximal enhancer elements as delineated in Extended Data Fig. 3a). Thus, all iPS cell efficiency and kinetic comparisons were conducted by using matched and validated pluripotency reporter systems.
Mansour, A. A. et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488, 409–413 (2012)
The online version of the original article can be found at 10.1038/nature12587