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Reply to “Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells”

Nature Genetics volume 42, pages 5–6 (2010)Cite this article

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Wen et al. reply:

Regarding microarrays, Filion and van Steensel claim that variations between undifferentiated and differentiated ES cells are due to sample labeling or hybridization conditions. Our extensive experience with microarray data is that variation due to hybridization and labeling can be controlled by appropriately normalizing the data. Our group included expert statisticians and spent a great deal of time and thought on the statistical analysis. Our method was based on a completely data-driven procedure, as described in the Supplementary Methods section of the paper. 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). Comparing various tissue-specific LOCKs using this same procedure revealed an extremely strong relationship between our statistical criteria of LOCKs and domain-specific gene silencing. We did consider other percentiles (cutoffs), and the conclusion that differentiated cells had more LOCKs did not change (Supplementary Fig. 2).

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Figure 1: Replicate data support differences of LOCKs between undifferentiated and differentiated ES cells.

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Authors and Affiliations

  1. Center for Epigenetics Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Bo Wen, Hao Wu, Rafael A Irizarry & Andrew P Feinberg

  2. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Bo Wen & Andrew P Feinberg

  3. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

    Hao Wu & Rafael A Irizarry

  4. Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto, Japan

    Yoichi Shinkai

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  1. Bo Wen
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  2. Hao Wu
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  3. Yoichi Shinkai
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  4. Rafael A Irizarry
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  5. Andrew P Feinberg
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Correspondence to Andrew P Feinberg.

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Wen, B., Wu, H., Shinkai, Y. et al. Reply to “Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells”. Nat Genet 42, 5–6 (2010). https://doi.org/10.1038/ng0110-5

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