Table 3. Candidate imprinted genes expressed with significant PO bias in TSCs.
| Gene | Chr | Coords | S | CB.1 | CB.2 | CB.3 | BC.1 | BC.2 | BC.3 | CBp | BCp | B | SNPs | RPKM |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Id1 | chr2 | 152562009-152563146 | + | 43.1 (31, 41) | 33.5 (52, 103) | 35.3 (55, 101) | 35.2 (32, 59) | 35.5 (39, 71) | 15.4 (14, 77) | 2.E-02 | 9.E-04 | P | 4 | 16.0 |
| R74862* | chr7 | 150207688-150239273 | − | 65.8 (25, 13) | 87.7 (71, 10) | 82.5 (99, 21) | 58.3 (21, 15) | 72.4 (63, 24) | 72.0 (67, 26) | 1.E-07 | 1.E-02 | M | 98 | 0.27 |
| Tsci1* | chr8 | 83383307-83405773 | + | 0.0 (0, 41) | 0.7 (1, 148) | 0.7 (1, 143) | 0.0 (0, 40) | 12.5 (10, 70) | 9.5 (13, 124) | 3.E-40 | 3.E-15 | P | 82 | 0.16 |
| Tsci2* | chr11 | 12051323-12097365 | + | 57.6 (19, 14) | 85.7 (48, 8) | 77.1 (37, 11) | 95.5 (21, 1) | 93.5 (87, 6) | 97.9 (93, 2) | 8.E-04 | 1.E-16 | M | 75 | 0.08 |
| AK017220 | chr11 | 51003334-51033915 | − | 3.6 (6, 159) | 2.2 (3, 134) | 0.7 (1, 137) | 4.8 (4, 79) | 56.3 (117, 91) | 7.2 (15, 192) | 3.E-44 | 4.E-03 | P | 161 | 2.10 |
| Tsci3 | chr11 | 51033968-51061895 | + | 3.9 (5, 123) | 3.1 (9, 280) | 0.3 (1, 285) | 4.4 (2, 43) | 46.9 (207, 234) | 9.6 (42, 396) | 7.E-54 | 4.E-04 | P | 101 | 0.32 |
| AK010368* | chr11 | 97459824-97484207 | + | 0.7 (1, 133) | 1.5 (6, 407) | 0.7 (3, 451) | 1.5 (1, 64) | 37.0 (101, 172) | 47.4 (451, 500) | 5.E-92 | 3.E-02 | P | 150 | 4.40 |
| Tsci4* | chr12 | 82108796-82120245 | − | 5.6 (1, 17) | 0.0 (0, 40) | 0.0 (0, 45) | 0.0 (0, 10) | 15.4 (2, 11) | 48.3 (14, 15) | 3.E-17 | 5.E-02 | P | 52 | 0.04 |
| Tsci5* | chr12 | 110730857-110753078 | − | 100.0 (2, 0) | 100.0 (8, 0) | 100.0 (16, 0) | 100.0 (6, 0) | 100.0 (12, 0) | 100.0 (34, 0) | 2.E-07 | 1.E-10 | M | 35 | 0.03 |
| Pdgfb | chr15 | 79826305-79845238 | − | 41.3 (250, 356) | 42.2 (1999, 2737) | 38.6 (2126, 3380) | 27.9 (58, 150) | 48.8 (2928, 3070) | 44.2 (3471, 4375) | 6.E-03 | 4.E-02 | P | 97 | 62.3 |
| Tsci6* | chr15 | 96980667-96997795 | − | 7.8 (17, 200) | 19.7 (12, 49) | 3.5 (12, 333) | 0.3 (1, 386) | 0.9 (6, 662) | 0.9 (9, 1032) | 8.E-18 | 5.E-103 | P | 129 | 0.75 |
| 1700010i14rik | chr17 | 9181197-9201184 | + | 100.0 (18, 0) | 84.0 (21, 4) | 90.7 (39, 4) | 100.0 (9, 0) | 100.0 (33, 0) | 70.1 (47, 20) | 8.E-11 | 2.E-03 | M | 43 | 0.81 |
| Qk | chr17 | 10399335-10512226 | − | 55.2 (235, 191) | 56.4 (648, 501) | 55.2 (574, 465) | 70.2 (342, 145) | 64.3 (687, 381) | 63.9 (565, 319) | 7.E-03 | 1.E-04 | M | 176 | 36.2 |
| Pacrg | chr17 | 10595877-11033057 | − | 75.0 (3, 1) | 92.9 (13, 1) | 86.7 (13, 2) | 100.0 (5, 0) | 90.0 (9, 1) | 84.6 (11, 2) | 1.E-04 | 9.E-04 | M | 29 | 0.21 |
| Park2 | chr17 | 11033249-12256226 | + | 86.8 (105, 16) | 81.3 (74, 17) | 85.7 (60, 10) | 61.1 (33, 21) | 76.5 (78, 24) | 73.6 (53, 19) | 9.E-18 | 3.E-03 | M | 273 | 0.08 |
| Mas1 | chr17 | 13033870-13061009 | − | 100.0 (6, 0) | 100.0 (63, 0) | 99.2 (123, 1) | 100.0 (2, 0) | 100.0 (34, 0) | 100.0 (12, 0) | 2.E-27 | 4.E-10 | M | 55 | 0.27 |
| Dact2 | chr17 | 14332236-14340838 | − | 59.6 (56, 38) | 56.9 (357, 270) | 54.5 (486, 405) | 83.2 (84, 17) | 71.4 (401, 161) | 70.8 (685, 283) | 3.E-03 | 6.E-07 | M | 40 | 7.65 |
Column annotations are the same as in Table 2. Coordinates given are relative to UCSC’s mm9 genome build. PO, parent-of-origin; TSC, trophoblast stem cell; SNP, single-nucleotide polymorphism; RPKM, reads per kilobase of transcript per million aligned reads.