FISH Validation of a Subset of WSSD Duplication-Positive C57BL/6J BACs
WSSD duplicated regions | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Accession | Clone | Length | MGSCv3 best placement | Size (bp) | Read depth (#/5 kb) | Divergent read ratio | Copy # | Cytogenetic position | FISH results description | ||
| AL929496.8 | RP23-3D2 | 254072 | chrX:21967539 | 251,000 | 1,403.9 | 21.4 | 5 | chrX_A3 | Intra Cluster | ||
| AC124400.4 | RP24-357O21 | 191219 | chr14:35800505 | 48,512 | 469.4 | 10.0 | 3 | chr14_C | Intra Cluster | ||
| AC124511 | RP23-440I16 | 179914 | chr12:1838950 | 179,000 | 440.2 | 6.4 | 4 | chr12_A2 | Inter + Intra interspersed (pericentromeric) | ||
| AC122877.3 | RP23-115K1 | 186549 | chr14:42943941 | 88,459 | 204.0 | 4.9 | 4 | chr14_B | Intra Cluster | ||
| AC124452.4 | RP24-219N2 | 177600 | chr7:23230794 | 177,961 | 611.8 | 4.4 | 2 | chr7_A2 | Intra Cluster (pericentromeric) | ||
| AL671630.8 | RP23-327E13 | 173610 | chrX:12967423 | 149,000 | 384.7 | 3.1 | 3 | chrX_F3 | Intra Cluster | ||
| AC087780.19 | RP23-324b17 | 206924 | chr1:88368502 | 99,000 | 192.2 | 3.0 | 2 | chr1_C-D;A2 | Intra Interspersed | ||
| AL627326.16 | RP23-20A22 | 184504 | chr4:27153628 | 95,000 | 163.9 | 2.8 | 4 | chr13_A2 | Intra Interspersed (pericentromeric) | ||
| AC098741.2 | RP23-122J17 | 211681 | chr12:97659614 | 146,818 | 134.8 | 2.3 | 2 | chr12_F1 | Intra Cluster | ||
| AL691445.21 | RP23-67G3 | 189233 | chrX:58776354 | 99,000 | 128.8 | 1.9 | 1 | chrX_D | Unique | ||
| AL606987.11 | RP23-38314 | 212647 | chr4:144269068 | 206,000 | 447.1 | 1.8 | 5 | chr4_E2 | Intra Cluster (telomeric) | ||
| AL731676.5 | RP23-460B8 | 180106 | chrX:116982329 | 71,542 | 155.9 | 1.8 | 1 | chrX_F2,3 | Unique | ||
| AC122796.3 | RP24-347J6 | 166768 | chr7:23230794 | 21,117 | 85.0 | 1.5 | 3 | chr7_A3 | Intra Cluster | ||
| AL731663.12 | RP23-360J20 | 181033 | chr4:144011588 | 180,000 | 391.2 | 1.4 | 5 | chr4_E2 | Intra Cluster (telomeric) | ||
| AC087166.3 | RP23-354D10 | 210476 | chr12:109410281 | 49,000 | 87.7 | 1.3 | 1 | chr12_F2 | Unique | ||
| AL451076.14 | RP23-43O20 | 203581 | chrX:2344144 | 47,000 | 271.8 | 1.2 | 2 | chrX_A3 | Intra *weak 2nd signal | ||
| AC126273.3 | RP23-99P15 | 182698 | chr13:23632869 | 182,130 | 122.0 | 1.1 | 4 | chr13_A3 | Intra Cluster | ||
| AC026767.30 | RP23-328L8 | 193167 | chr7:48547102 | 76,116 | 83.9 | 1.1 | 2 | chr7_C | Intra Cluster | ||
| AC046145.16 | RP23-306D24 | 188606 | chr7:48296368 | 37,000 | 80.8 | 1.0 | 1 | chr7_B | Unique | ||
| AL732405.8 | RP23-149P4 | 193425 | chrX:87422908 | 45,000 | 109.0 | 1.0 | 2 | chrX_C,D | Intra Cluster | ||
| AL808115.7 | RP23-224M8 | 163408 | chr17:9981377 | 56,000 | 77.3 | 1.0 | 1 | chr17_A2 | Unique (pericentromeric) | ||
| AL713974.8 | RP23-135I10 | 191603 | chrX:40294317 | 77,001 | 72.0 | 0.8 | 2 | chrX_A5 | Intra Cluster | ||
[i] A subset of mouse BAC clones with large (>20 kb) regions of duplication by WSSD detection were subsequently examined by FISH (Methods; 17/22 were confirmed as duplicated). The best placement within MGSCv3 was determined by similarity searches. Estimated copy number by FISH for tight tandem clusters was based on signal intensity compared with a unique hybridizing probe. The results of all FISH experiments are available online (http://www.biologia.uniba.it/mouse/).