Figure 1

Study summary. This study explores methodological aspects related to interpretation of allele specific expression (ASE) from RNAseq data, as well as a broader question of local and cis-eQTL matching and their correspondence to independent set of identified DNase I peaks. A. Experimental approach to allele specific expression. Four pooled F1 samples from males and females of BxD and DxB crosses were sequenced. Allele specific counts for each SNP in each sample were produced in a table form, and treated as independent replicates in analysis by DEseq package. B. Summary of previous local-eQTL studies and the performed comparisons. Hybrid Mouse Diversity Panel is a panel of 95 inbred and recombinant inbred strains, that was previously used for mapping local-eQTLs at ~5 Mb resolution. F2 cross refers to 465 male and female mice that were produced from B and D strains, and allowed a lower resolution local-eQTL mapping. C. In the final part of this study we compared cis and local-eQTLs to DNase I peaks, which potentially mark cis acting elements and to previously published ASE from another tissue. DNase I peak illustration was adapted form [21].