Supplementary web site for

Digital DNA methylation analysis of stem cell reprogramming by targeted bisulfite sequencing
Jie Deng, Robert Shoemaker, Bin Xie, Athurva Gore, Emily Leproust, Jessica Antosiewica-Bourget, Dieter Egli, Nimet Maherali, In-Hyun Park, Junying Yu, George Daley, Kevin Eggan, Konrad Hochedlinger, James Thomson, Wei Wang, Yuan Gao, Kun Zhang.


Methylation data in BED format.

Note: These files can be visualized using the Human Genome Brower Gateway (http://genome.ucsc.edu/cgi-bin/hgGateway) by loading all the files as custom tracks.
Alternatively, each of the files can be loaded to the Genome Browser using the following web links:

1.      BJ

2.      IMR90

3.      IMR90_2

4.      hFib2

5.      BJ-iPS11

6.      BJ-iPS12

7.      IMR90-iPS

8.      hFib2-iPS

9.      Hues6-BJ-Hybrid1

10.  Hues12

11.  Hues42

12.  Hues63

To quickly navigate to the 26 selected genes or the 8 ENCODE regions, the chromosome coordinates in Supplementary Table 2 can be copied/pasted to the “position/search” window of the UCSC Genome Browser.


Raw Illumina GA sequencing reads.


Perl scripts

Please contact Dr. Kun Zhang (kzhang _at_ bioeng.ucsd.edu) for questions.