Distinct epigenetic features of differentiation-regulated replication origins

Table 1 Characterization of replication origins in cancer and non-cancer cells

Row #	Cell line	# of All origins	# Shared origins	# of Cell-specific origins	% Shared	% Cell specific
1	ES	90,621	62,477	8507	68.9	9.4
2	EB	144,753	65,868	18,366	45.5	12.7
3	AS_iPS	119,944	67,977	14,896	56.7	12.4
4	PWS_iPS	135,397	76,642	16,471	56.6	12.2
5	K562	202,653	64,972	35,266	32.1	17.4
6	MCF7	193,118	62,930	26,100	32.6	13.5
7	HCT116	78,859	57,873	1319	73.4	1.7
8	U2OS	92,814	60,631	3955	65.3	4.3

Replication origins were identified as regions enriched in nascent strand reads in four non-cancer cell lines (ES, EB, AS_iPS and PWS_iPS) and in four cancer cell lines (K562, MCF7, HCT116, U2OS). The number of replication origins is the number of origin peaks called versus the appropriate genomic control for each cell line (see “Methods” section and Additional file 1 for details and reproducibility data). The number of shared origins is the number of origin peaks that were present in the indicated cell line and in all other cells of the same group (non-cancer cells for ES, EB and the two iPS lines and cancer cells for K562, MCF7, HCT116 and U2OS). The number of cell-specific origins is the number of origin peaks that were present in the reference cell line, but not in any of the other cells of the same group. The “% shared” peaks and the “% cell-specific” peaks represent the percentage of shared and cell-specific peaks, respectively, versus the overall number of peaks in the indicated file

ISSN: 1756-8935