. 2016 Feb 18;6:21134. doi: 10.1038/srep21134

Table 2. The 22 variants selected for RT-PCR validation.

	Gene	Chr	Pos	dbSNP id	SNV type	Ref	Alt	Sample or individual^§	icd-ASE			Static ASE
	Gene	Chr	Pos	dbSNP id	SNV type	Ref	Alt	Sample or individual^§	ΔASE_RNA-seq p-value	ΔASE_RNA-seq amp	ΔASE_RT-PCR amp	ASE_RNA-seq p-value	ASE_RNA-seq amp	ASE_RT-PCR amp
icd-ASE	PDE4DIP	1	144873887	rs1699787	syn	C	T	9	7.9e-07	−1.88	−5.2^#
	RALB	2	121050989	rs1065518	3’UTR	T	A	1	1.4e-02	0.83	0.2
	DFNA5	7	24758753	rs754555^*	syn	C	T	4	3.5e-08	−2.32	−2.9^#
	MS4A7	11	60152563	rs950803	syn	T	A	3	1.3e-05	1.21	1.3^#
	CTSC	11	88045583	rs217086^*	non-syn	A	G	2	1.9e-84	3.39	4.6^#
	LILRB1	19	55148487	rs8101605^*	3’UTR	G	A	9	2.5e-12	−1.71	−2.1^#
	LILRB2	19	54782919	rs386056	non-syn	C	T	6	2.0e-08	−1.07	−1.6^#
	LILRB2	19	54784130	rs383369	non-syn	T	C	6	1.7e-13	−1.33	−1.3^#
Static ASE	GBP3	1	89474818	rs17433780^*	non-syn	A	G	8_T				6.0e-101	−0.26	0.4
	GBP3	1	89479063	rs4656077^*	non-syn	G	A	8_T				3.5e-47	0.20	−1.4
	NOTCH2NL	1	145282405	rs2596058	3’UTR	T	C	8_U				1.1e-04	0.24	6.2^#
	NOTCH2NL	1	145282904	rs28713400	3’UTR	A	G	6_U				2.1e-05	0.26	5.1^#
	ZDBF2	2	207174316	rs3732084^*	syn	T	C	3_T				1.1e-05	0.50	10.3^#
	ZDBF2	2	207178422	rs1448902^*	3’UTR	G	A	3_T				8.7e-07	0.50	7.5^#
	KCNMB3	3	178978604	rs7429685^*	intronic	T	G	2_U				4.1e-41	0.49	14.4^#
	KCNMB3	3	178978689	rs62410373^*	intronic	A	G	2_U				1.9e-12	0.45	0.9
	SLC12A7	5	1057615	rs2241606^*	syn	A	G	2_U				2.6e-11	0.29	−0.2
	SLC12A7	5	1081767	rs4526148^*	non-syn	C	T	2_U				1.4e-09	−0.31	2.3
	EPSTI1	13	43542677	rs7324030^*	intronic	C	A	3_T				3.8e-05	0.39	−1.8
	SYNM	15	99670518	rs1670227^*	non-syn	T	C	7_T				2.7e-25	−0.43	−4.2^#
	SYNM	15	99672722	rs2292288^*	non-syn	A	G	7_T				7.1e-16	0.42	7.2^#
	CPNE7	16	89663072	rs659974^*	3’UTR	G	A	4_T				9.9e-03	−0.35	−8.5^#

(#) Cases where the RT-PCR data validated the RNA-seq data (true positives). (*) SNV interrogated by SNP-array (heterozygous in the individual chosen for validation). (§) Sample chosen for validation and for which ASE amplitudes and p-value are shown. N_U and N_T refer to the untreated and LPS treated samples, respectively, of individual N. ASE_RNA-seq amplitude (amp) for static ASE and ΔASE_RNA-seq for icd-ASE are defined in Eq.1 and Eq 2, respectively (Methods). ASE_RT-PCR refers to the difference in cycle-threshold between the two alleles and ΔASE_RT-PCR = ASE_RT-PCR(T) − ASE_RT-PCR(U), where T and U corresponds to the treated and untreated condition. ASE_RNA-seq p-values: static ASE (modified binomial test), icd-ASE (Fisher’s exact test). P-values were Benjamini-Hochberg multiple testing corrected. Chr, chromosome; Pos, SNV coordinate on chromosome; Ref, reference allele; Alt, alternative allele; icd-ASE, individual condition-dependent ASE; SNV, single nucleotide variant; syn, synonymous exonic; non-syn, non-synonymous exonic; UTR, un-translated region.