Supporting information for embryonic stem cell culture, JASPAR prediction, and data summary.

The quality of embryonic stem cell cultures was monitored by quantification of differentiation using florescent staining and ImageJ analysis (Figure A). The nucleosome repeat length of embryonic stem cells was also measured via micrococcal nuclease digestion (Figure B). The JASPAR matrix and regions scanned to find predicted Oct4/Sox2 binding sites are presented in Figure C and the results of the analysis are presented in Table A. The quantification of TF occupancy, in vivo nucleosome occupancy, and in vitro nucleosome occupancy for each predicted binding site are summarized in Table B.
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