Table 1.
Summary statistics of library PET sequences
| Self-ligation | Intrachromosome inter-ligation |
Interchromosome inter-ligation |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Library Code |
Library identity |
Total PET | Unique PET |
PET |
*PET clusters |
PET |
^PET clusters |
PET |
^PET clusters |
| Small scale testing of the ChIA-PET method | |||||||||
| IHM001N | ChIA-PET | 715,369 | 271,648 | 78,706 | 2,701 | 16,677 | 176 | 176,265 | 0 |
| IHM001H | ChIA-PET | 764,899 | 293,754 | 103,740 | 3,405 | 17,718 | 215 | 172,296 | 0 |
| IHM043 | ChIP-PET | 1,118,509 | 745,251 | 634,993 | 1,158 | 7,386 | 2† | 102,872 | 1 |
| SHC007 | ChIP-PET | 361,241 | 214,668 | 192,511 | 489 | 2,196 | 0 | 19,961 | 0 |
| IHM062 | ChIA-PET (IgG) |
436,248 | 217,708 | 40,847 | 0 | 11,254 | 0 | 165,607 | 0 |
| Chimeras analysis | |||||||||
| IHH015M | ChIA-PET (AA+BB) |
4,246,429 | 2,049,719 | 953,384 | 3,909 | 129,492 | 2,183 | 966,843 | 3 |
| IHH015C | ChIA-PET (chimeras) |
5,904,476 | 1,790,714 | 15,490 | 35 | 98,805 | 0 | 1,676,419 | 0 |
| Large scale ChIA-PET analysis | |||||||||
| IHM001F | ChIA-PET | 31,828,194 | 4,638,633 | 1,249,081 | 14,560 | 234,400 | 1,451 | 3,155,152 | 15 |
| IHH015F | ChIA-PET | 19,590,581 | 6,125,099 | 1,841,684 | 6,665 | 348,057 | 3,543 | 3,935,358 | 4 |
Notes: ChA-PET data mapped at satellites and structural variation sites were removed.
*
Self-ligation PET clusters for identifying binding sites (FDR < 0.01, PET count ≥ 5).
^
Inter-ligation PET clusters for identifying interactions include at least 2 (small scale) or 3 (chimeras and large scale analysis) overlapping PETs (FDR < 0.05). Interchromosomal interactions were subjected to manual curation.
†
One interaction has a genomic span < 5 Kb, suggesting it results from extra-long self-ligation PETs, and the other has a genomic span >10 Mb and PET counts of only 2, and so could be non-specific.