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. Author manuscript; available in PMC: 2020 Sep 17.
Published in final edited form as: Methods Mol Biol. 2017;1488:75–120. doi: 10.1007/978-1-4939-6427-7_4

Fig. 9.

Fig. 9

Impact of variants overlapping probe sets in microarray data sets. SNPs overlapping Oprl1 probe set 1450486_a_at (perfect match or PM probes 299709 and 452573) lead to expression measurements that are higher in BXD strains that have inherited the B allele and lower in strains that have inherited the D allele. The QTL Heatmap reveals a strong eQTL with higher expression associated with inheritance of the B allele at the Oprl1 locus (blue) only for the probes that overlap SNPs. The arrowhead indicates the genomic position of the probes. No other probes demonstrate a strong association between inheritance of alleles at this locus and gene expression. This analysis reveals that the strong cis-eQTL detected for Oprl1 is actually the result of a technical artifact resulting from sequence variants that disrupt the hybridization of probes to their target RNA sequence in strains other than the reference B6 strain (in this case the D2 strain)