Table 1 |
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|
Primer sequences, regions examined for methylation, and the methods used to detect methylation |
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|
Region |
Method |
Position |
Size (bp) |
Forward primer (5'-3') |
Reverse primer (5'-3') |
Pyrosequencing primer (5'-3') |
|
|
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|
1 |
COBRA Bisulphite sequencing |
-966 to -733 |
233 |
AGTTTGGTTTYGGGYGATTTAT TTTGT |
CCCAAAAAACACCTATCTAAATA AACT |
|
|
|
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|
2 |
Bisulphite pyrosequencing |
-110 to +217 |
327 |
TTATGGTTGTAGTTTTYGAGAG GAGAGAAT |
CTACAAAAACCRCAACAAATAC AACTACAAACTAA (round 1) CCCAAACAACTACACTAAACAT ACTCAA (nested) |
GAGAGGAGAGAATTG |
|
|
||||||
|
3 |
COBRA Bisulphite sequencing |
-80 to +234 |
314 |
TTTAGTAGAGTTTGTGGTTTGG GGATTT |
CAAACTTCCATCATAACTACAA CTTCC |
|
|
|
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|
4 |
qMSP |
+237 to +368 |
132 |
AGTTGAGTCGTTGTGAGGCGA GGTCG |
CAAACCGACCGACTCCCCGAAAACG |
|
|
|
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|
5 |
Bisulphite sequencing |
+554 to +836 |
283 |
GTTGTAGTTTTAGGGAGGGGGT |
CRCCRCTACCAAACCTCTAACTACTA |
|
|
|
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|
6 |
Bisulphite sequencing Bisulphite pyrosequencing |
+801 to +971 |
171 |
GGTTTTTTTTGTAGGATGGAAA TGGT |
CRCCRCTACCAAACCTCTAACTACTA |
AAATGGTTTTGGATTT |
|
|
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|
Six regions of the PTEN CpG island were investigated for methylation in this study using various methods. Listed are the regions assayed, the method used for the detection of DNA methylation, the position of the region analysed relative to the transcription start site of the PTEN gene (NM_000314) located at Chr10:89613175 (NCBI36/hg18, March 2006 freeze), the size of each amplicon, and primer sequences (including pyrosequencing primer sequences) |
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|
Hesson et al. Biological Procedures Online 2012 14:5 doi:10.1186/1480-9222-14-5 |
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