Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

Q:

I am very interested in your recent work "Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells". Could you please advise with respect to the experimental datasets used in your study? I am now looking at the mouse ESC TFs dataset from Chen et al., 2008, provided in their supplemental Table S3. Could you please advise, whether these data refer to the mm8 mouse genome assembly or the mm9 mouse genome assembly? The row data deposited in GEO seem to be updated in 2012, so they are probably re-mapped to mm9. But do you know what was the initial genome build reported in this paper, mm8 or mm9? (For consistency I want to use the "original" peaks reported by Chen et al., and used in your study, not making peak calling again from their row data).

A:
We are pleased to know your interest on the paper. In terms of the Genome assembly, we were using mm8 as the original paper (Chen et al.).

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