Table 3.

Primer sequences

Locus	Forward	Reverse	Tann
Replication timing/ChIP
Gbe	GGTGCAGATCATCCCCTTGA	TTACCCGACGGCGAAAG	60
α-Globin	CCACAAGCTGCGTGTGGAT	ATGCCGCCTGCCAGGT	60
Oct4	GGGTGAGAAGGCGAAGTCTGAA	GTGAGCCGTCTTTCCACCAGG	55
Nanog	CCCTCTGAGTTTGACCGGTGA	CAAGCTAGGATGTTAGGTCTCCCTG	60
Esg1	AAAGACGAACACAGAGTCAAACACC	CACCTGCTCGATGTGAGACATTC	60
Zfp57	TGCAAGATAAGAACGAGGAGCAGGAG	CCTTTGCGGCTTTGTGGATTTGTG	60
Rex1	TTTGCGGGAATCCAGCAGT	CGTCCCATCGCCACTCTAGAC	55
Sox2	CCATCCACCCTTATGTATCCAAG	CGAAGGAAGTGGGTAAACAGCAC	55
Nkx2.9	AAGTGCGAGGCGCTCG	TGGCACCTTCCGGACTTG	60
Sox3	TGCCCAGATGGCTTCCTATT	ACCCGGACATTCTCCGCT	60
Mage a2	TTGGTGGACAGGGAAGCTAGGGGA	CGCTCCAGAACAAAATGGCGCAGA	60
Ebf	AGATCTGGTTGAAGCCCTGTATGG	CATGTCACATCTCAGATCCTGTGTTCT	60
Mash1	CCAGGCTGGAGCAAGGGA	CGGTTGGCTTCGGGAGC	55
β-Globin	GGTGAACTTTACTGCTGAGGAAAAG	TCACCACCAACCTCTTCAACAT	60
Myf5	GGAGATCCGTGCGTTAAGAATCC	CGGTAGCAAGACATTAAAGTTCCGTA	55
Math1	CCCTCACTCAGGTCGCCTG	CGTGCGAGGAGCCAATCA	55
Sox1	ACAAGAGGAGGCAGCGAACC	TCGCAGGTGGAAAGTTTCTCC	55
Msx1	ACAGAAAGAAATAGCACAGACCATAAGA	TTCTACCAAGTTCCAGAGGGACTTT	55
Frg1	AAGGAGCCTATATCCATGCACTGGAC	GCCTCCCTGCCATTGCTTGT	60
Slc7a2	GACAAGGAACAGGGCGAGAAG	CTTTCCTCATCCTGGGCTTGAGTA	60
Msr1	GCCACCAATGCCCTAGAATTTC	GGCAGGCTCTCACTAGGAAGC	60
Loc2	ACTAGCAACTGGACATAAGAGTACACTACC	ATTACATATGGTGTCTGGAAGCCAG	60
Adam 26	CCTTGAACAACGCCCTTTTGTG	GCAAGCTCCCAAAACAGGTGT	60
Loc4	TAAGGTAGGCAGTGAGAGACATCCA	GGTGTAAGAAGGTTAGAACTAA	60
X141	GGGTCATAAAACGCTTTTCCAGGAA	TAGCACTGGAGATCAGATTGACGCCT	60
Minor satellite	TGATATACACTGTTCTACAAATCCCGTTTC	ATCAATGAGTTACAATGAGAAACATGGAAA	55
Major satellite	GACGACTTGAAAAATGACGAAATC	CATATTCCAGGTCCTTCAGTGTGC	55
rDNA	CCTGTGAATTCTCTGAACTC	CCTAAACTGCTGACAGGGTG	60
IAP	TTGATAGTTGTGTTTTAAGTGGTAAATAAA	AAAACACCACAAACCAAAATCTTCTAC	60
LINE 1	TTTGGGACACAATGAAAGCA	CTGCCGTCTACTCCTCTTGG	60
SINE B1	GTGGCGCACGCCTTTAATC	GACAGGGTTTCTCTGTGTAG	60
Gene expression
Mage a2	GAAGATCTCAGGAGTGTCAGGACTG	TCAGCCATTATGACTGTCCTAGGTAA	60
Ubc	AGGAGGCTGATGAAGAGCTTGA	TGGTTTGAATGGATACTCTGCTGGA	60
Oct4	CCCAAGGTGATCCTCTTCTGCTT	GAGAAGGTGGAACCAACTCCCG	60
CpG methylation assay
Major sat	GACGACTTGAAAAATGACGAAATC	CATATTCCAGGTCCTTCAGTGTGC	55
Sox2	TGGACTGCGAACTGGAGAAGG	CGCCCGGAGTCTAGCTCTAAATATT	60

IAP, intracisternal A particle. T_ann, annealing temperature.