Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks

Ling, King-Hwa; Hewitt, Chelsee A; Tan, Kai-Leng; Cheah, Pike-See; Vidyadaran, Sharmili; Lai, Mei-I; Lee, Han-Chung; Simpson, Ken; Hyde, Lavinia; Pritchard, Melanie A; Smyth, Gordon K; Thomas, Tim; Scott, Hamish S

doi:10.1186/1471-2164-15-624

Table 3 Summary of spatiotemporal RT-qPCR validations of 25 selected DEGs

From: Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks

Official symbol	Full gene name (ID)	Probe set ID	Log₂expression of Ts1Cje normalized against disomic littermates
			Microarray analysis				RT-qPCR analysis
			P1	P15	P30	P84	P1	P15	P30	P84
Cerebral Cortex
Atp5o	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	1437164_x_at	0.58	0.71	0.72*	0.64	1.07	0.78*	0.28	0.77*
Brwd1	Bromodomain and WD repeat domain containing 1	1433955_at	0.55	0.53	0.63	0.86*	0.44	0.44	0.70*	0.6
Brwd1	Bromodomain and WD repeat domain containing 1	1452322_a_at	0.07	0.62	0.47	0.83*	0.44	0.44	0.70*	0.6
Donson	Downstream neighbor of SON	1426739_at	0.76	0.72	0.91**	0.78	0.89	0.61	0.70*	0.73
Dopey2	Dopey family member 2	1428330_at	0.68*	0.47	0.61	0.45	0.53	0.42	0.52*	0.56
Erdr1	Erythroid differentiation regulator 1	1452406_x_at	0.61	-1.14	5.61*	1.82	0.54	-0.64	5.85*	2.16
Ifnar1	Interferon (alpha and beta) receptor 1	1449026_at	0.8	0.8	1.17*	1.29*	0.63	0.57	0.44	0.66*
Ifnar2	Interferon (alpha and beta) receptor 2	1451462_a_at	0.7	0.9	0.99*	0.98	0.36	0.41	0.45	0.91*
Itgb8	Integrin beta 8	1436223_at	-0.88	-1.02	-1.21**	-0.7	-0.59	-0.90*	-0.95*	-0.88*
Itsn1	Intersectin 1 (SH3 domain protein 1A)	1452338_s_at	0.58	0.96	1.42**	1.66**	0.43	0.88	0.69*	0.57*
Morc3	Microrchidia 3	1420091_s_at	0.55	0.81**	0.64	0.66	0.7	0.39	0.59	0.78
Mrps6	Mitochondrial ribosomal protein S6	1424440_at	0.84**	0.62	0.73	0.35	1.11	0.49	0.57	0.54
Sod1	Superoxide dismutase 1, soluble	1440222_at	1.79*	1.47	1.41	1.79	0.13	0.07	-0.15	-0.16
Tmem50b	Transmembrane protein 50B	1423707_at	0.78**	0.51	0.70*	0.46	1.12	0.62	0.56*	0.77*
Ttc3	Tetratricopeptide repeat domain 3	1448361_at	0.45	0.45	0.54*	0.43	0.78	0.68	0.45	0.45*
Cerebellum
Atp5o	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	1416278_a_at	0.43	0.67**	0.82*	0.54	0.90	0.47	0.40	0.36
Atp5o		1437164_x_at	0.68*	0.74**	0.78	0.59	0.90	0.47	0.40	0.36
Brwd1	Bromodomain and WD repeat domain containing 1	1427322_at	0.32	0.81*	0.84*	0.54	0.33	0.98	0.54*	0.42
		1433955_at	1.17***	0.81**	0.57	1.01***
		1452322_a_at	0.14	0.37	0.22	0.94***
Cbr1	Carbonyl reductase 1	1460196_at	0.71	0.52	0.30	0.72*	0.58	0.67*	0.31	0.25
Donson	Downstream neighbor of SON	1426739_at	0.82*	0.91**	0.75	0.75*	0.34	1.09	0.46	0.37
Dopey2	Dopey family member 2	1428330_at	0.58	0.83**	0.70*	0.59	0.50	0.65	0.52*	0.36
Erdr1	Erythroid differentiation regulator 1	1452406_x_at	0.67	-0.73	5.69*	1.34	-0.11	-0.31	4.63*	1.36
Hmgn1	High mobility group nucleosomal binding domain 1	1422495_a_at	0.22	0.96**	0.49	0.68*	0.43	0.69	0.26	0.48
		1438940_x_at	0.40	0.76*	0.24	0.54
		1455897_x_at	0.49	1.07**	0.30	0.80
Ifnar1	Interferon (alpha and beta) receptor 1	1442222_at	0.45	1.12*	0.73	0.68	0.55	0.60	0.44	0.70*
Ifnar1	Interferon (alpha and beta) receptor 1	1449026_at	0.55	0.67	0.85	1.10*	0.55	0.60	0.44	0.70*
Ifnar2	Interferon (alpha and beta) receptor 2	1451462_a_at	0.61	0.90*	0.80	0.93*	0.53	0.62	0.44	0.80
Ifngr2	Interferon gamma receptor 2	1423558_at	0.67**	0.14	0.17	0.21	0.86	0.53	0.17	0.32*
Itgb8	Integrin beta 8	1436223_at	-0.61	-1.35***	-1.22**	-1.54***	-0.52	-1.05*	-0.47	-1.69***
Itsn1	Intersectin 1 (SH3 domain protein 1A)	1421192_a_at	0.03	0.94*	1.16**	0.66	0.19	0.65	0.34	0.29
		1435885_s_at	0.46	1.18*	0.25	0.50
		1452338_s_at	0.44	0.99	0.80	1.30**
Kcnj6	Potassium inwardly-rectifying channel, subfamily J, member 6	1451868_at	-0.07	0.95	1.23*	0.33	0.31	0.79	0.32	0.16
Morc3	Microrchidia 3	1420091_s_at	0.78**	0.84***	0.69*	0.55	0.17	0.46	0.24	0.59
Morc3	Microrchidia 3	1452224_at	0.82	0.99	1.21*	0.52	0.17	0.46	0.24	0.59
Mrps6	Mitochondrial ribosomal protein S6	1424440_at	0.89**	0.70*	0.89**	1.00***	0.97	0.74*	0.05	0.66*
Mrps6	Mitochondrial ribosomal protein S6	1447585_s_at	1.13*	0.88	0.53	0.94	0.97	0.74*	0.05	0.66*
Paxbp1	PAX3 and PAX7 binding protein 1	1418007_at	0.55	1.32*	0.59	0.80	0.27	0.69	0.66*	0.38
Paxbp1	PAX3 and PAX7 binding protein 1	1418008_at	0.56	1.45*	0.63	0.75	0.27	0.69	0.66*	0.38
Smim11	Small integral membrane protein 11	1417402_at	0.90*	0.69	0.59	0.59	-0.24	0.76	-0.13	-0.39
Sod1	Superoxide dismutase 1, soluble	1440222_at	1.60	1.24	1.40	1.96**	0.15	0.17	0.06	-0.17
Son	Son cell proliferation protein	1420952_at	0.36	1.28*	0.71	0.87	0.39	1.23	0.63*	0.44
		1435862_at	0.35	1.04**	1.24**	0.78
		1437924_at	0.28	0.96**	0.75	0.67
Stat1	Signal transducer and activator of transcription 1	1420915_at	-0.30	0.40	0.06	1.03**	-0.34	0.03	0.57	0.62
Tbata	Thymus, brain and testes associated	1450281_a_at	0.22	0.97*	-0.03	0.25	0.57	0.81*	0.57	0.47
Tmem50b	Transmembrane protein 50B	1423707_at	0.83**	0.69*	1.07***	0.71**	0.83	0.62	0.46	0.42
Ttc3	Tetratricopeptide repeat domain 3	1416484_at	0.60	0.39	0.74	0.87*	0.59	0.36	0.66*	0.38
Wrb	Tryptophan rich basic protein	1460446_at	0.72*	0.90**	0.45	0.67*	0.61	0.66	0.68*	0.37
Hippocampus
Actg1	Actin, gamma, cytoplasmic 1	1415779_s_at	-0.02	-0.07	-0.07	0.39*	-0.16	-0.02	-0.02	0.18
Atp5o	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	1416278_a_at	0.68	0.37	0.48	1.09***	0.64	0.23	0.39	0.59
Atp5o		1437164_x_at	0.71*	0.64*	0.74*	0.94***	0.64	0.23	0.39	0.59
Brwd1	Bromodomain and WD repeat domain containing 1	1427322_at	0.78	0.26	0.52	1.11***	0.66	-0.36	0.33	0.45
		1433955_at	0.39	0.70*	0.70*	0.91***
		1452322_a_at	0.67*	0.46	0.68*	0.22
Cbr1	Carbonyl reductase 1	1460196_at	0.64	0.95**	0.72	0.74*	0.24	0.30	0.42	0.61*
Donson	Downstream neighbor of SON	1426739_at	0.81*	0.65	0.63	0.92**	-0.08	0.34	0.34	0.89**
Dopey2	Dopey family member 2	1428330_at	1.00***	0.68*	0.85**	0.77**	0.57	-0.16	0.55*	0.55
Erdr1	Erythroid differentiation regulator 1	1439200_x_at	0.68	-0.94	4.72*	0.80	0.51	-1.27	5.36*	1.68
Erdr1	Erythroid differentiation regulator 1	1452406_x_at	0.80	-1.12	5.77*	1.10	0.51	-1.27	5.36*	1.68
Hmgn1	High mobility group nucleosomal binding domain 1	1422495_a_at	0.36	0.16	0.64	0.82**	0.04	0.10	0.51	0.31
Ifnar1	Interferon (alpha and beta) receptor 1	1449026_at	0.46	1.12*	0.84	0.75	-0.08	0.25	0.41	0.57*
Ifnar2	Interferon (alpha and beta) receptor 2	1427691_a_at	0.73	1.49*	0.91	0.50	0.07	0.08	0.43	0.50
		1440169_x_at	1.22	1.49*	0.84	0.62
		1451462_a_at	0.81	0.83	0.92*	1.43***
Itgb8	Integrin beta 8	1436223_at	-1.19**	-0.64	-1.04*	-1.14**	-1.11	-1.26**	-0.92*	-0.80*
Itsn1	Intersectin 1 (SH3 domain protein 1A)	1421192_a_at	1.01*	0.48	0.97*	1.04**	0.38	-0.23	0.36	0.73*
Itsn1	Intersectin 1 (SH3 domain protein 1A)	1425899_a_at	0.76	-0.54	0.18	1.67*	0.38	-0.23	0.36	0.73*
Kcnj6	Potassium inwardly-rectifying channel, subfamily J, member 6	1425707_a_at	-0.21	0.57	1.07*	-0.06	0.96	0.17	0.07	0.66
Morc3	Microrchidia 3	1420091_s_at	0.64*	0.66*	0.78**	0.99***	-0.16	0.31	0.45	0.85*
Morc3	Microrchidia 3	1452224_at	1.20*	0.51	0.55	1.45**	-0.16	0.31	0.45	0.85*
Mrps6	Mitochondrial ribosomal protein S6	1424440_at	0.77*	0.72*	0.64	0.91**	0.46	0.50	0.55	0.38
Mrps6	Mitochondrial ribosomal protein S6	1447585_s_at	0.61	1.15*	0.91	0.61	0.46	0.50	0.55	0.38
Son	Son cell proliferation protein	1435862_at	0.99*	0.20	0.58	1.17**	0.73	0.07	0.44	0.84**
Tmem50b	Transmembrane protein 50B	1423707_at	0.96***	0.76**	0.84*	0.99***	0.78	-0.01	0.61*	0.61
Ttc3	Tetratricopeptide repeat domain 3	1448361_at	0.33	0.63**	0.45	0.46	0.34	0.37	0.50	0.37
Wrb	Tryptophan rich basic protein	1460446_at	0.56	0.85**	0.69	0.70*	1.00	0.26	0.44	0.63*

All selected DEGs are trisomic genes located on chromosome 16 except for Erdr1 (a disomic gene located on chromosome X), Itgb8 (a monosomic gene located on chromosome 12), Sod1 (a trisomic gene located on chromosome 16, although one of the copies is non-functional due to truncation), and Stat1 (a disomic gene located at chromosome 1).
*p<0.05, **p<0.01 and ***p<0.001 based on Empirical Bayes t-statistic test.

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