GCB-7 FLJ21062 45% methylated CpGs in 19 clones; PMR: 72
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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.
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Transcript of GCB-7 FLJ21062 45% methylated CpGs in 19 clones; PMR: 72
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.
GCB-7 FLJ2106245% methylated CpGs in 19 clones; PMR: 72
89%
0%
78%
100%
89% 78%
89%
67%
100%
0%
0%
0%
100%
56%
0%
0%
0%
0%
0%
ABC-6 FLJ210620.5% methylated CpGs in 23 clones; PMR: 0
0%
11%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0% 0%
0%
0%
0%
0% 0%
0%
0%
0%
ABC-7 FLJ21062 2% methylated CpGs in 19 clones; PMR: 0
0%
0%
0%
0%
0%
0%
0%
0% 33%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
GCB-15 FLJ21062 0.4% methylated CpGs in 26 clones; PMR: 8
0%
0%
0%
0%
0%
0%
0%
0%
11%
0%
0%
0%
0% 0%
0%
0%
0%
0%
0%
0% 0%
0%
0%
0%
0%
0%
GCB-3 FLJ21062 4% methylated CpGs in 19 clones; PMR: 0
*=AG
*
*
*
*
*
0%
22%
0%
0%
0%
0%
0%
0%
0%
22%
11%
0%
11%
0%
0%
0%
0% 0%
0%
ABC-8 FLJ21062 19% methylated CpGs in 22 clones; PMR: 0
44%
44% 56%
0%
0%
44%
0%
56%
0%
78%
0%
0%
0%
44%
0%
0%
56%
0%
0% 0%
0%
0%
GCB-10 FLJ2106273% methylated CpGs in 37 clones; PMR: 104
78%
78% 89%
78% 89% 89% 67%
100% 89% 89%
56%
78% 100%
67%
100% 0% 78% 89% 78% 78%
67%
0%89%
78%
0%
67% 67% 78%
89% 67% 78%
89% 67%
78% 78%
67% 78%
ABC-4 FLJ2106216% methylated CpGs in 14 clones; PMR: 0
0%
0%
0%
0%
0%
0%
0%
0%100%
22%
100%
0%
0%
0%
PBL_DNA-Donor1 FLJ210620.4% methylated CpGs in 27 clones; PMR: 0
0%
0%
11%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0% 0%
0%
0%
0%
0%
0%
0%
PBL_DNA-Donor4 FLJ21062 1.5% methylated CpGs in 22 clones; PMR: 0
22%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0%
0% 0%
0%
11%
GCB-5 ONECUT2 4% methylated CpGs in 17 clones; PMR: 0
0%
0%
6%
29%
0%
0%
0%
0%
29%
0%
0%
0%
0%
0%
0%
0%
6%
GCB-7 ONECUT2 69% methylated CpGs in 31 clones; PMR: 82
100%
100%100%
18% 94% 0%
94% 94%100%100% 94%
6% 94% 24%100%100% 0%100% 0%100% 94% 0% 94% 88% 88%100% 59%
0%100%100%
0%
ABC-6 ONECUT278% methylated CpGs in 24 clones; PMR: 69
100%
100%
0%
100%
100%
88%
0%
100%
94%
100%
100%
100%
100%
0%
100%
94%
100%
100%
94%
6%
94%
100%
0%
94%
ABC-7 ONECUT2 65% methylated CpGs in 24 clones; PMR: 137
35%
88%
88%
100%
0%
88%
100%
100%
88%
6%
0%
94%
0%
88%
94%
100%
12%
6%
88%
94%
100%
0%
100%
94%
ABC-9 ONECUT2 70% methylated CpGs in 41 clones; PMR:111
100%
100%
0%
94% 6%
88% 0%
94% 0% 94%
100% 82% 0% 94% 71%
0% 94%
100% 94%
0% 0% 12%
94% 94% 88%
100%100%
94%
100% 82% 82%
94%
82%
100% 82% 88% 94%
94%
0%
94%
88%
GCB-4 ONECUT253% methylated CpGs in 28 clones; PMR:51
24%
100%100%
0% 0%
94%
0%
0% 0%
0%
12% 94%
0%100%
100%100%
0%
100%
6%
100%
100%100%100%100% 6% 12%
100%
24%
ABC-2 ONECUT2 71% methylated CpGs in 27 clones; PMR: 64
100%100%100% 94% 65%
0%76%
94%100%
76%0%
88%100%100%100%100% 94% 76% 76%100% 0% 0%100% 94% 71% 0% 0%
GCB-10 ONECUT2 93% methylated CpGs in 34 clones; PMR:135
100%
94%100%
94%100% 100%
100% 0%100%100%
100%
100%
100%
100%100%100% 0%100%100%100% 88%100%100%100% 94%100%100%100%
88% 88%100%100%100%100%
PBL_DNA-Donor1 ONECUT2 2% methylated CpGs in 17 clones; PMR: 0
6%
0%
0%
0%
6%
0%
0%
0%
0%
6%
6%
0%
12%
0%
0%
6%
0%
PBL_DNA-Donor4 ONECUT2 7% methylated CpGs in 20 clones; PMR: 1
6%
0%
29%
18%
0%
0%
0%
0%
0%
0%
35%
24%
0%
0%
18%
0%
18%
0%
0%
0%
