Table 1.
Summary of DNA methylation mapping experiments
| Run. No. | Method | Sample name | #lanes | #reads (total) |
#reads (aligned) |
Alignment rate |
#reads (unique) |
#reads (duplicates) |
Unique read rate |
|---|---|---|---|---|---|---|---|---|---|
| 1 | MeDIP | HUES6 ES cell line | 2 | 37,086,239 | 22,798,831 | 61.5% | 12,849,623 | 9,949,208 | 56.4% |
| 2 | MeDIP | HUES8 ES cell line | 2 | 36,078,308 | 24,266,670 | 67.3% | 12,287,174 | 11,979,496 | 50.6% |
| 3 | MeDIP | Primary colon tumor | 2 | 33,453,797 | 18,582,183 | 55.5% | 7,006,484 | 11,575,699 | 37.7% |
| 4 | MeDIP | Matched normal colon tissue | 2 | 37,789,936 | 21,793,567 | 57.7% | 10,360,103 | 11,433,464 | 47.5% |
| Run. No. | Method | Sample name | #lanes | #reads (total) |
#reads (aligned) |
Alignment rate |
#reads (unique) |
#reads (duplicates) |
Unique read rate |
|---|---|---|---|---|---|---|---|---|---|
| 5 | MethylCap | HUES6 ES cell line | 3 | 38,436,495 | 23,401,511 | 60.9% | 21,712,433 | 1,689,078 | 92.8% |
| 6 | MethylCap | HUES8 ES cell line | 3 | 38,735,596 | 21,670,301 | 55.9% | 19,585,988 | 2,084,313 | 90.4% |
| 7 | MethylCap | Primary colon tumor | 3 | 37,718,830 | 23,206,054 | 61.5% | 21,600,129 | 1,605,925 | 93.1% |
| 8 | MethylCap | Matched normal colon tissue | 3 | 38,330,519 | 22,724,002 | 59.3% | 21,290,282 | 1,433,720 | 93.7% |
| Run. No. | Method | Sample name | #lanes | #reads (total) |
#reads (aligned) |
Alignment rate |
#CpGs (total) | #CpGs (unique) |
Mean CpG coverage |
|---|---|---|---|---|---|---|---|---|---|
| 9 | RRBS | HUES6 ES cell line | 2 | 30,004,147 | 12,150,905 | 40.5% | 22,181,147 | 2,181,128 | 10.2× |
| 10 | RRBS | HUES8 ES cell line | 2 | 28,395,040 | 12,670,034 | 44.6% | 29,704,332 | 2,185,751 | 13.6× |
| 11 | RRBS | Primary colon tumor | 4 | 40,015,958 | 9,545,423 | 23.9% | 16,891,325 | 1,297,296 | 13.0× |
| 12 | RRBS | Matched normal colon tissue | 4 | 32,072,287 | 6,214,732 | 19.4% | 10,190,227 | 1,134,963 | 9.0× |
| Run No. | Method | Sample name | #arrays | #CpGs (total) | #CpGs (valid) | #CpGS (unique) |
Valid probe rate |
|---|---|---|---|---|---|---|---|
| 13 | Infinium | HUES6 ES cell line | 1 | 27,578 | 27,192 | 27,192 | 98.6% |
| 14 | Infinium | HUES8 ES cell line | 1 | 27,578 | 27,090 | 27,090 | 98.2% |
| 15 | Infinium | Primary colon tumor | 1 | 27,578 | 27,561 | 27,561 | 99.9% |
| 16 | Infinium | Matched normal colon tissue | 1 | 27,578 | 27,478 | 27,478 | 99.6% |
Technical notes: (i) Between two and four lanes [#lanes] were sequenced on the Illumina Genome Analyzer II, which yielded approximately 30 to 40 million 36-basepair, singled-end reads [#reads (total)] per sample and method. These reads were aligned to the human genome [# reads (aligned)], and the number of unique [#reads (unique)] as well as duplicate reads [#reads (duplicates)] was calculated by counting the first read that aligns to a specific genomic position as unique and all further occurrences of the same genomic position as duplicates (genomic positions were defined by the combination of chromosome, read start position and strand). (ii) Three lanes were sequenced for samples 5–8, one lane per eluate (high, medium and low, as described in the Methods section). (iii) Samples 11 and 12 were part of a sequencing optimization run that resulted in lower sequencing yield and reduced alignment rates. Four lanes were sequenced to reach the target of 30 to 40 million reads per sample and method. (iv) All other samples were sequenced on two lanes each. There were no failed runs that had to be redone, and all sequencing data that were generated for the current project are summarized in this table. (v) The yield of a single lane of Illumina Genome Analyzer II sequencing strongly increased during the course of this study. As of June 2010, we observe total read numbers per lane that average around 40 million for MeDIP and MethylCap, and which are close to 30 million for RRBS. Current alignment rates range from 60% to 80% for typical runs with all three methods.