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Fig. 3 | BMC Genomics

Fig. 3

From: The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits

Fig. 3

DAE QTLs and differential gene expression in the forebrain of B6/129SF1 mice and parental strains. a The 129S Gabra2 allele was over-represented in reciprocal crosses when assayed either by RNA-Seq or by Sanger Sequencing. b qPCR in forebrain of the parental B6 and 129S strains shows that Gabra2 is more highly expressed in the 129S strain. These data suggest the presence of a cis-acting regulatory element at Gabra2 that is allelically variable between the two strains. c The B6 Gas5 allele was over-represented in reciprocal crosses when assayed either by RNA-Seq or by Sanger Sequencing. a, c In RNA-Seq data, total numbers of reads of all SNVs in a gene were added up and then significance of DAE in the total number of reads was assessed by a binomial test. False Discovery Rate (FDR) adjusted p-values were obtained by the Benjamini-Hochberg method. The allele signals from the Sanger cDNA sequencing results were normalized using the allele-specific peak ratios from the Sanger gDNA sequencing. To test if the B6 allele and 129S allele were equally expressed, Sanger sequencing data were evaluated by a one-tailed t-test with values of B6 allele area/(B6 allele area + 129S allele area). **P < 0.005 and *P < 0.05 (d) qPCR analysis of forebrain of the parental B6 and 129S strains showed that Gas5 is more highly expressed in the B6 strain. (B,D) Data of qPCR are the means ± SEM of 4 or 5 mice of each 129S1/SvlmJ and C57BL/6 J. **P < 0.005 and *P < 0.05 by a two-tailed t-test. These data suggest the presence of a cis-acting regulatory element at Gas5 that is variable between the two strains, however (e) the presence of a 1 bp deletion in the 5’-UTR of 129S transcript may lead to transcript instability resulting in the observed allelic expression imbalance in F1’s and difference in expression between parental strains, as discussed

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