Table 2 Known imprinted genes expressed with significant PO bias in TSCs
GeneChrCB.1CB.2CB.3BC.1BC.2BC.3CBpBCpBSNPsRPKM
AK076687achr25.3 (10, 180)4.5 (26, 557)0.4 (2, 551)1.1 (2, 185)1.8 (5, 269)0.7 (3, 439)5E-376E-62P2261.03
Sfmbt2chr22.3 (144, 6233)8.4 (790, 8599)1.6 (290, 17804)1.0 (79, 7694)1.5 (299, 19439)1.0 (217, 22508)8E-312E-50P109278.8
Nespasachr20.0 (0, 94)0.0 (0, 251)2.2 (5, 223)0.0 (0, 88)4.0 (8, 191)0.6 (1, 161)4E-512E-30P342.58
Phf17chr332.4 (665, 1387)30.3 (2099, 4819)46.8 (1568, 1786)13.8 (130, 809)24.7 (1483, 4515)15.5 (820, 4457)2E-032E-18P32148.2
Sgcechr64.5 (11, 231)8.8 (78, 809)6.6 (47, 666)2.9 (4, 135)6.3 (60, 890)3.7 (33, 870)1E-681E-52P31919.9
Peg10chr60.1 (18, 12098)0.2 (226, 149701)0.3 (310, 123681)0.1 (4, 3763)0.3 (507, 150895)6.0 (4951, 78040)0E+004E-10P29793
Mestchr60.0 (0, 16)1.7 (3, 175)0.3 (11, 3209)0.4 (2, 447)0.5 (13, 2780)1.1 (71, 6602)3E-1174E-105P4265.1
Peg3chr70.2 (7, 4413)0.1 (21, 24916)0.2 (44, 19674)0.5 (17, 3529)19.6 (4032, 16588)41.4 (10215, 14486)1E-3022E-02P10775.2
Usp29chr74.1 (4, 94)1.7 (14, 829)2.2 (8, 361)2.2 (1, 44)16.9 (76, 374)42.3 (80, 109)2E-874E-04P2372.56
D7ertd715eachr70.0 (0, 86)0.0 (0, 313)0.0 (0, 243)0.0 (0, 95)1.1 (2, 176)0.0 (0, 78)4E-693E-37P645.96
Snrpnchr70.0 (0, 48)0.5 (1, 208)1.4 (2, 146)9.1 (1, 10)2.0 (2, 97)7.7 (3, 36)3E-452E-14P9713.6
H19achr795.5 (2508, 119)95.4 (8222, 394)95.7 (15727, 714)98.8 (61749, 756)99.6 (170049, 742)51.3 (173851, 164950)7E-2422E-03M92432
Ascl2chr792.6 (50, 4)89.9 (519, 58)86.1 (352, 57)100.0 (10, 0)81.6 (476, 107)96.2 (101, 4)1E-406E-08M413.6
Cd81chr767.0 (254, 125)90.3 (1678, 181)80.9 (2438, 576)72.3 (225, 86)79.5 (2277, 587)81.5 (2043, 465)8E-113E-17M7487.8
Tssc4chr765.3 (47, 25)82.7 (382, 80)79.1 (453, 120)60.9 (53, 34)75.6 (436, 141)69.6 (385, 168)1E-142E-04M93.30
Kcnq1ot1achr70.2 (1, 544)0.2 (2, 1139)5.3 (56, 1010)0.3 (1, 349)0.5 (3, 580)0.0 (0, 305)9E-188E-87P3710.99
Cdkn1cchr799.7 (1185, 3)100.0 (9367, 4)99.8 (6716, 13)100.0 (351, 0)76.5 (6925, 2123)99.9 (2673, 4)0E+009E-06M3335
Slc22a18chr788.5 (46, 6)89.8 (264, 30)88.7 (235, 30)92.9 (13, 1)72.6 (244, 92)98.7 (155, 2)6E-332E-04M1416.75
Phlda2chr7100.0 (120, 0)100.0 (4921, 1)99.3 (3279, 24)95.7 (112, 5)72.2 (3611, 1392)98.7 (1211, 16)2E-551E-06M2290
Gab1chr815.3 (342, 1896)18.3 (1745, 7809)14.8 (1624, 9329)9.2 (129, 1275)24.8 (2367, 7163)16.8 (1575, 7804)3.E-662.E-12P63358.3
Plagl1chr100.0 (0, 86)0.4 (2, 528)1.0 (2, 202)0.0 (0, 19)1.3 (4, 297)4.2 (4, 91)4E-761E-27P1421.15
Grb10chr1168.8 (1527, 691)89.1 (5640, 692)85.0 (5615, 994)98.2 (1849, 33)92.0 (8908, 777)86.4 (6314, 994)5E-147E-12M455159
Zrsr1chr110.0 (0, 131)0.4 (1, 225)0.4 (1, 273)0.0 (0, 33)21.4 (69, 254)1.9 (6, 312)4E-724E-08P74.86
Grb10asachr1169.9 (51, 22)87.9 (94, 13)92.9 (79, 6)97.3 (36, 1)88.7 (94, 12)87.2 (75, 11)4E-081E-12M1230.08
Dlk1chr12100.0 (2, 0)99.5 (195, 1)93.1 (297, 22)100.0 (2, 0)93.8 (45, 3)98.1 (53, 1)2E-182E-10P151.47
Meg3achr1299.3 (438, 3)70.0 (7, 3)97.6 (290, 7)99.9 (1392, 1)99.8 (3325, 5)99.9 (11062, 8)2E-696E-126M10985.3
Mirgachr12100.0 (159, 0)100.0 (10, 0)93.1 (54, 4)100.0 (772, 0)100.0 (716, 0)99.8 (2007, 4)1E-244E-150M11911.4
Pde10achr1790.9 (251, 25)88.3 (878, 116)85.6 (600, 101)97.1 (34, 1)73.8 (479, 170)77.0 (349, 104)5E-641E-06M4483.10
Slc22a3chr17100.0 (41, 0)98.2 (667, 12)93.6 (612, 42)23.1 (3, 10)96.7 (353, 12)96.8 (91, 3)9E-401E-02M1432.05
Airnachr174.3 (28, 628)0.4 (19, 5256)0.4 (18, 4213)1.6 (6, 370)1.4 (47, 3304)0.8 (11, 1362)2E-309E-124P4433.01
Igf2rchr1797.9 (1011, 22)98.6 (2650, 38)98.4 (3821, 63)97.8 (723, 16)98.6 (3348, 48)98.8 (4743, 57)1E-1992E-111M33073.0
Igf2chr745.8 (2694, 3186)32.5 (22266, 46340)29.0 (20372, 49913)8.2 (71, 790)46.9 (17649, 19980)75.9 (24740, 7869)1E-46E-1NS211418
  • Gene ID and chromosomal location are listed. For each CB.x and BC.x cell line, the percent of allele-specific reads mapping to the maternally inherited chromosome is shown. In that same column, the absolute number of maternal and paternal SNP-overlapping read counts detected in each TSC line, respectively, are shown in parentheses. P-values for corresponding PO biases in CB.x and BC.x cell lines were corrected for multiple testing via Benjamini Hochberg, and are listed under “CBp” and “BCp” columns, respectively. B, parental direction of PO bias: P, paternally biased; M, maternally biased; NS, not significantly biased. PO, parent-of-origin; TSC, trophoblast stem cell; SNPs, single-nucleotide polymorphisms—the number of distinct SNPs covered by RNA-Seq reads for the respective transcript. RPKM, average allele-nonspecific RPKM (reads per kilobase of transcript per million aligned reads) of each respective transcript across the 6 profiled TSC lines; lncRNA, long noncoding RNA.

  • a Known or putative lncRNAs.