Supplemental table 1. Primers for deep bisulfite sequencing and limiting dilution bisulfite sequencing

Gene / Primera / Sequence (5'-3') / Amplicon length (bp) / Number of CpGs / Chromosomal localization (bp)b / Gene structure
DBS
GTL2 / forward / CTT GCT TCC TGG CAC GAG GGG TGT AAA AAG TTA TTT GGG ATT AG / 347 / 8 / Chr. 14: 101,275,633-101,275,945 / DLK1-GTL2 intergenic (primary) DMR
reverse / CAG GAA ACA GCT ATGA CAC CAA AAT ACT AAC TAC TCC TTA AAC A
PEG3 / forward / CTT GCT TCC TGG CAC GAG GAG GTT GTT GAT TGG TTA GTA TAG AAG / 265 / 19 / Chr. 19: 57,351,943-57,352,173 / Primary DMR,
5' UTR
reverse / CAG GAA ACA GCT ATG ACA CTC ACC TCA CCT CAA TAC TAC
OCT4 / forward / CTT GCT TCC TGG CAC GAG GGG GTT TGG TGA AAT GAG G / 344 / 5 / Chr. 6: 31,138,421-31,138,730 / 5' Upstream promoter
reverse / CAG GAA ACA GCT ATG ACA CTC CAC TAC ACT CCA ATC TA
NANOG / forward / CTT GCT TCC TGG CAC GAG GGA ATA TGG TTT AAT AGG AATG GGA TAA / 313 / 8 / Chr. 12: 7,941,483-7,941,761 / 5' Upstream promoter
reverse / CAG GAA ACA GCT ATG ACA CCT CTA CCT CCC AAA TTC AA
LD
GTL2 / outer forward / GAA TTA TAG GGA ATG ATG GTG TA / 188 / Chr. 14:101,275,634-101,275,822 / DLK1-GTL2 intergenic DMR
outer reverse / CCA AAA TAC TAA CTA CTC CTT AAA CA
inner forward / AGG GTT AGG AAG TTT AGT AGG TTA / 150
inner reverse* / ACT ACT CCT TAA ACA AAA AAA CAC ATA AT / Chr. 14:101,275,645-101,275,795
sequencing / GTA GTA AAT TAA AGT GTA TTA GAG A / 5
PEG3 / outer forward / GGT TGT TGA TTG GTT AGT ATA G / 229 / Chr. 19: 57,351,942-57,352,171 / Primary DMR,
5' UTR
outer reverse / CAC TCA CCT CAC CTC AAT AC
inner forward / GGT GTA GAA GTT TGG GTA GTT G / 153
inner reverse* / CTC ACC TCA CCT CAA TAC TAC / Chr. 19: 57,351,944-57,352,097
sequencing / TGT TTA TTT TGG GTT GGT / 3
SNRPN / outer forward / GGG TTT TAG GGG TTT AGT AGT / 337 / Chr. 15: 25,199,962-25,200,299 / Primary DMR,
Intronic CpG island
outer reverse / ACT CCA AAT CCT AAA AAC TTA AAA TATC
inner forward* / AGG GAG TTG GGA TTT TTG TAT T / 237 / Chr. 15: 25,200,012-25,200,249
inner reverse / CCC AAA CTA TCT CTT AAA AAA AAC
sequencing 1 / ACA CAA CTA ACC TTA CCC / 3
sequencing 2 / CCA ACC TAC CTC TAC / 3
LIT1 (assay 1) / forward / GTT ATT TTAT ATT TAG TTA GTG TTT TAT G / 306 / Chr. 11: 2,721,164-2,721,470 / Primary DMR,
intronic CpG island
outer reverse / ACA AAA TCT TAC TAA AAA ACT CCC TAA A
inner reverse* / CTA AAA AAC TCC CTA AAA ATC / 295 / Chr. 11: 2,721,175-2,721,470
sequencing 1 / GGG GGT AGT YGG AG / 2
sequencing 2 / TGT YGT TTA ATT AGT AGG TGG G / 6
LIT1 (assay 2) / outer forward / GGG AGA ATA GTG TTG AGG AGT TT / 621 / Chr. 11: 2,720,690-2,721,311 / Primary DMR
outer reverse / CCC TAC TAC CCC CCA ATC AAC AAA TAA
inner forward / GGG GAG GAT TAA GTT GAG AGG TA / 201 / Chr. 11: 2,721,110-2,721,311
inner reverse* / CCC TAC TAC CCC CCA ATC AAC AAA TAA
sequencing / GGA GTT TTT TGG AGG / 6
OCT4 / outer forward / AGA AGG ATT GTT TTG GTT TAG TAG A / 330 / Chr. 6: 31,138,451-31,138,781 / 5' Upstream promoter
outer reverse / AAC TAC TCA ACC CCT CTC T
inner forward / AAG TTT TTG TGG GGG ATT TGT AT / 185 / Chr. 6: 31,138,482-31,138,667
inner reverse* / CCA CCC ACT AAC CTT AAC CTC TA
sequencing / TGA GGT TTT GGA GGG / 2
NANOG / outer forward / TAG AGT AAT TTA GAT TAG GTG GGG AAT / 262 / Chr. 12: 7,941,607-7,941,869 / 5' Upstream promoter
outer reverse / TAA CCA AAC TAA TTT CAA ACT CCT AAC TT
inner forward / GGA ATA TGG TTT AAT AGG AAT GGG ATA A / 154 / Chr. 12: 7,941,607-7,941,761
inner reverse* / TAA CCA AAC TAA TTT CAA ACT CCT AAC T
sequencing 1 / ATT TTT GTA ATT TTA GTA AAT TGG G / 2
sequencing 2 / TTT TAA AAA TTA AGA AAA AGG T / 3
BOLL / outer forward / TTT TTG AGG GTT TGG AGG / 501 / Chr. 2: 198,650,141-198,650,642 / 5’ UTR CpG island
outer reverse / CAA TCC TCC TTC ACT TCC CC
inner forward / TGT GTT ATG GGG GTT AGA AAG G / 361 / Chr. 2: 198,650,158-198,650,519
inner reverse* / CCC AAA TCC ACC CTA ACT AAC TT
sequencing / TGT TAT GGG GGT TAG AAA / 5
CATSPER1 / outer forward / ATG GGG ATA ATT GAA GTT TAT TTG AT / 400 / Chr. 11: 65,789,822-65,7902,22 / Promoter flanking CpG island, CTCF
outer reverse / ACT CAC TTA ATC CTC ACC C
inner forward* / AGT GTT TAG AAT GGA GTT TGA GAT AG / 336 / Chr. 11: 65,789,883-65,790,219
inner reverse / CAC TTA ATC CTC ACC CCT AAA AAA TAA AT
sequencing 1 / CAT CTA CT CCA AAT AT / 4
sequencing 2 / AAA AAC TAA ACC CTC C / 2

aBiotinylated primers for pyrosequencing are indicated by *.

bAccording to Ensembl release 75 of February 2014.