1. Supplementary Figure 3. Bisulfite sequencing of FLJ21062 and ONECUT2 CpG islands. The relative positions of the forward (left-most) and reverse (right-most) PCR primers as well as the methylation-specific reporter oligonucleotide used in FLJ21062 HB-442 and ONECUT2 HB-446 MethyLight reactions are provided along with the sample number (ABC = ABC-DLBCL and GCB = GCB-DLBCL). The primers used in these sequencing analyses were:
5'-ATTAGAGGTTTGGGTTAATTGGG-3' (FLJ21062 forward) and
5'-AAAAAAAACAACCTAAAAATC-3' (FLJ21062 reverse) and
5'-AGGAGTATAGAAATTTTTTGTGTGG-3' (ONECUT2 forward) and
5'-ACCTAAACATTTTACCCCTCTAAA -3' (ONECUT2 reverse).
Light gray and blackened circles respectively denote methylated and unmethylated CpG dinucleotides in each clone. The percentage of methylated CpGs in all clones and total number of clones sequenced are provided above each panel along with the corresponding MethyLight PMR value. In addition, the percentage of methylated CpGs in a given clone is provided to the right of each clone. Note that the forward primer of the FLJ21062 HB-442 MethyLight reaction is not show since it falls outside of the amplicon used for bisulfite sequencing.

2. 45% methylated CpGs in 19 clones; PMR: 72
GCB-7 FLJ21062
45% methylated CpGs in 19 clones; PMR: 72
89% 0%
78%
100%
67%
56%

3. 0.5% methylated CpGs in 23 clones; PMR: 0
ABC-6 FLJ21062
0.5% methylated CpGs in 23 clones; PMR: 0 0%
11%

4. 2% methylated CpGs in 19 clones; PMR: 0
ABC-7 FLJ21062
2% methylated CpGs in 19 clones; PMR: 0 0%
33%

5. 0.4% methylated CpGs in 26 clones; PMR: 8
GCB FLJ21062
0.4% methylated CpGs in 26 clones; PMR: 8 0%
11%

6. 4% methylated CpGs in 19 clones; PMR: 0
GCB-3 FLJ21062
4% methylated CpGs in 19 clones; PMR: 0 * 0%
22%
11%
*=AG

7. 19% methylated CpGs in 22 clones; PMR: 0
ABC-8 FLJ21062
19% methylated CpGs in 22 clones; PMR: 0
44%
56% 0%
78%

8. 73% methylated CpGs in 37 clones; PMR: 104
GCB FLJ21062
73% methylated CpGs in 37 clones; PMR: 104
100% 0%
78%
89%
78%
78%
67%
67%
78%
67%
78%
89%
89%
67%
89%
67%
78%
100%
89%
89%
89%
67%
56%
78%
78%
78%
78%
89%
78%
100%
67%
78% 0%
67%
89% 0%
78%

9. 16% methylated CpGs in 14 clones; PMR: 0
ABC-4 FLJ21062
16% methylated CpGs in 14 clones; PMR: 0 0%
100%
22%

10. 0.4% methylated CpGs in 27 clones; PMR: 0
PBL_DNA-Donor1 FLJ21062
0.4% methylated CpGs in 27 clones; PMR: 0 0%
11%

11. 1.5% methylated CpGs in 22 clones; PMR: 0
PBL_DNA-Donor4 FLJ21062
1.5% methylated CpGs in 22 clones; PMR: 0
22% 0%
11%

12. 4% methylated CpGs in 17 clones; PMR: 0
GCB-5 ONECUT2
4% methylated CpGs in 17 clones; PMR: 0 0% 6%
29%

13. 69% methylated CpGs in 31 clones; PMR: 82
GCB-7 ONECUT2
69% methylated CpGs in 31 clones; PMR: 82
100%
18%
94% 0% 6%
24%
88%
59%

14. 78% methylated CpGs in 24 clones; PMR: 69
ABC-6 ONECUT2
78% methylated CpGs in 24 clones; PMR: 69
100% 0%
88%
94% 6%

15. 65% methylated CpGs in 24 clones; PMR: 137
ABC-7 ONECUT2
65% methylated CpGs in 24 clones; PMR: 137
35%
88%
100% 0% 6%
94%
12%

16. 70% methylated CpGs in 41 clones; PMR:111
ABC-9 ONECUT2
70% methylated CpGs in 41 clones; PMR:111
100%
88% 0%
94%
100%
82%
71%
12%
100% 0% 6%
94%

17. 53% methylated CpGs in 28 clones; PMR:51
GCB-4 ONECUT2
53% methylated CpGs in 28 clones; PMR:51 0%
12%
94%
100% 6%
24%
24%
100%
100% 0% 0%
94% 0% 0% 0% 6%
12%
100%

18. 71% methylated CpGs in 27 clones; PMR: 64
ABC-2 ONECUT2
71% methylated CpGs in 27 clones; PMR: 64
100%
94%
65% 0%
76%
88%
71%

19. 93% methylated CpGs in 34 clones; PMR:135
GCB ONECUT2
93% methylated CpGs in 34 clones; PMR:135
100%
94% 0%
88%

20. 2% methylated CpGs in 17 clones; PMR: 0
PBL_DNA-Donor1 ONECUT2
2% methylated CpGs in 17 clones; PMR: 0 0% 6%
12% 6% 0%

21. 7% methylated CpGs in 20 clones; PMR: 1
PBL_DNA-Donor4 ONECUT2
7% methylated CpGs in 20 clones; PMR: 1 6% 0%
29%
18%
35%
24%