Table 1. Genes having differential expression either between strains or among different embryonic days.

Gene* number	Name	Description	Gene† Group	Start	Fold‡ E14.5	Fold‡ E16.5	Fold‡ E18.5	Bonadj§ strain	Bonadj§ Eday
111	Pycard	PYD and CARD domain containing Gene	II	135135617	−2.29	−1.67	−1.79	0.0003	0.0595
124	Inpp5f	inositol polyphosphate-5-phosphatase F	II	135754842	1.90	1.69	2.30	0.0036	1.0000
47	Tbx6	T-box 6	II	133924997	2.38	2.09	2.89	0.0055	1.0000
16	D430042O09Rik-204	RIKEN cDNA D430042O09 gene	II	132851390	3.94	2.61	3.65	0.0073	1.0000
9	Nsmce1-003	non-SMC element 1 homolog	I	132611154	5.54	3.58	7.09	0.0084	1.0000
150	telomerase	NM_009354.1	IV	73764438	3.99	2.14	3.87	0.0085	1.0000
8	Nsmce1-002	non-SMC element 1 homolog	I	132611154	2.52	2.05	3.57	0.0122	1.0000
26	Nfatc2ip	nuclear factor calcineurin-dependent 2 interacting protein	II	133526368	1.68	1.69	2.05	0.0125	1.0000
55	Taok2	TAO kinase 2	II	134009192	1.65	1.38	1.97	0.0143	1.0000
110	B230325K18Rik	RIKEN cDNA B230325K18	II	135126593	9.69	4.68	7.75	0.0165	1.0000
91	1700120K04Rik	RIKEN cDNA 1700120K04 gene	II	134747592	3.37	1.99	2.35	0.0177	1.0000
80	9130019O22Rik	RIKEN cDNA E430018J23 gene	II	134525774	3.63	2.28	3.78	0.0190	1.0000
87	1700008J07Rik	non-coding RNA	II	134655683	2.64	1.87	3.05	0.0202	1.0000
120	BC017158	UPF0420 protein C16orf58 homolog	II	135414893	1.56	1.43	1.67	0.0226	1.0000
140	Vegfa188	vascular endothelial growth factor A	III	46153942	1.88	1.45	2.05	0.0236	1.0000
88	Phkg2	phosphorylase kinase, gamma 2	II	134716854	1.70	1.34	2.19	0.0250	1.0000
19	D430042O09Rik-209	RIKEN cDNA D430042O09 gene	II	132851390	2.04	2.09	5.63	0.0284	1.0000
41	Giyd2	GIY-YIG domain containing 2	II	133832982	1.57	1.63	2.40	0.0291	1.0000
54	Ino80e	INO80 complex subunit E	II	133995094	4.64	2.71	3.79	0.0343	1.0000
127	Dock1	dedicator of cytokinesis 1	II	141862370	1.87	2.15	2.47	0.0384	1.0000
122	Tial1	Tia1 cytotoxic granule-associated RNA binding protein-like 1	II	135583291	2.02	1.54	2.12	0.0418	1.0000
109	Fus	malignant liposarcoma gene	II	135110971	1.47	1.49	1.72	0.0428	0.6911
40	Sult1a1	sulfotransferase family 1A, phenol-preferring, member 1	II	133816379	−2.29	1.01	1.76	1.0000	0.0026
129	Angpt2	angiopoietin 2	III	18690263	−1.15	1.14	1.61	1.0000	0.0077
139	Tgfb1	Transforming gr factor β binding protein 1	III	75404869	1.30	1.18	1.32	0.1245	0.0087
37	Nupr1	nuclear protein 1	II	133766763	−1.72	1.21	1.70	1.0000	0.0096
65	Qprt-001	quinolinate phosphoribosyltransferase	II	134250628	−1.55	−1.19	1.10	1.0000	0.0377
20	AC150648.2	GSG1-like	II	133024217	−1.59	−1.28	−1.27	1.0000	0.0448

Expression assay by NanoString nCounter. 3 RNA samples of pia at each time point for each strain, with each sample composing of ≥8 embryos from ≥2 litters (18 samples, ∼200 embryos). Transcript number for each gene normalized to mean transcript number for 6 housekeeping genes: βactin, Gapdh, Tubb5, Hprt1, Ppia, Tbp.

^*Gene number same as in Figure 6 and Table S2.

^† I, genes in EMMA region; II, genes in 95% CI of Chr 7 QTL; III, angiogenic-related genes located elsewhere in genome; IV, proliferation-related genes located elsewhere in genome.

^‡Fold change for Bc vs B6 if positive and B6 vs Bc if negative.

^§Bonferroni-adjusted p values (p-value÷150, for 150 genes/splice forms assayed) from 2-way ANOVA for 2 strains (20 genes p<0.05) and 3 embryonic days (6 genes p<0.05).