Figure 1.

Reproducibility and tissue specificity of ASE measured with NSR-seq. (a) Observed and expected error in biological replicates. RNA was isolated from independent samples, and subjected to NSR-seq (see methods). The error was calculated as the difference in log2(allelic ratio) between the two replicates, and is shown in relation to the average number of reads for the SNP in the two replicates (left panel). As expected, SNPs with more reads show lower error. The theoretically expected errors from the binomial distribution (right panel). Simulated data was not significantly different than the real data, when comparing errors by the Wilcoxon test (p > 0.2). (b) Ratio of allele-specific sequencing reads between two biological replicates for RefSeq genes with at least 100 reads. R2 = 0.84 (n = 289, p = 2.4e-115) (c) ASE conservation of RefSeq genes between islets and adipose. log(binomial-p) reflects confidence of ASE, and was arbitrarily set to negative when bias was toward B6 allele. R2 = 0.20 (n = 887, p = 2.4e-115)

Babak et al. BMC Genomics 2010 11:473   doi:10.1186/1471-2164-11-473
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