METHYL-SEQ PROCESSED DATA

Data is shown for each of the 90,612 Methyl-seq regions

column1	region chromosome		
column2	region start coordinate		
column3	region end coordinate		
column4	number of MspI sites above threshold in region		
column5	region length (bp)		
column6	#CpGs in region		
column7	CpG density of region (#CpGs in region/length of regions in bp)		
column8	0=MspI tag count above threshold (Library1)	HCT116	Msp I MethylSeq
column9	methylation call, Library2, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	HCT116	Hpa II MethylSeq
column10	methylation call, Library3, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	HCT116	Hpa II MethylSeq
column11	methylation call meDIP (library4)  NOTE 0=methylated (tag average>1), 1=unmethylated (tag average<=1)	HCT116	meDIPSeq
column12	methylation call, Library5, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 hESC	Hpa II MethylSeq
column13	methylation call, Library6, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 endoderm	Hpa II MethylSeq
column14	methylation call, Library7, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 AFP+ hESC-derived cells	Hpa II MethylSeq
column15	methylation call, Library8, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 AFP- hESC-derived cell negative	Hpa II MethylSeq
column16	methylation call, Library9, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 embryoid bodies	Hpa II MethylSeq
column17	methylation call, Library10, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 conditioned medium	Hpa II MethylSeq
column18	methylation call, Library11, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	H9 EB-derived cells	Hpa II MethylSeq
column19	methylation call, Library12, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	BG02 hESC	Hpa II MethylSeq
column20	methylation call, Library13, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	BG02 EB-derived cells	Hpa II MethylSeq
column21	methylation call, Library14, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	BG02 EB-derived cells	Hpa II MethylSeq
column22	methylation call, Library15, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	fetal liver 11 weeks	Hpa II MethylSeq
column23	methylation call, Library16, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	fetal liver 24 weeks	Hpa II MethylSeq
column24	methylation call, Library17, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)	adult liver	Hpa II MethylSeq  
column25	region overlaps CpG island? (yes or no)		
column26	region overlaps 7x Regulatory Potential?  (yes or no)		
column27	region classification (promoter=PROM, 5'UTR, coding exon=CODING, 3'UTR, INTRON, intergenic=INTGEN)		
column28	Refseq id for overlapping gene		
column29	Gene symbol for overlapping gene		
column30	region overlaps with histone modifications (bivalent, H3K4_only, H3K27_only, neither)		
column31	region overlaps with promoter classifications (HCP, ICP, LCP, NA)		
column32	list of MspI/HpaII sites in region		

Brunner, A. L., Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen. L., Chiao, E., Oyolu, C. B., Schroth, G. P., Absher, D., Baker, J. C. and Myers, R. M.  (2009).  Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.  Genome Res.  In press.