Figure 1: Evaluation of cDNA-smMIPs for estimation of differential expression with artificial transcripts.
From: Quantification of differential gene expression by multiplexed targeted resequencing of cDNA
(a) Outline of the approach. (b) Accuracy of differential expression estimates from 337 individual cDNA-smMIPs targeting 92 ERCC transcripts in condition ERCC1 and ERCC2. The 92 transcripts are divided into four groups; for each group the difference in transcript abundance between condition ERCC1 and ERCC2 is known, and is indicated by the solid lines. Four technical capture replicates were performed on respectively one cDNA sample for condition ERCC1 and one cDNA sample for condition ERCC2. The expression value for each smMIP is estimated using a Bayesian model. Data points are coloured according to their expected expression fold difference. (c) Comparison of differential expression quantification by cDNA-smMIPs and the previously published method CaptureSeq5 that performs targeted RNA-Seq by biotin-labelled oligonucleotide hybridization. Only transcripts with log2-expression values of >4 were included for both methods. Differential expression estimated with the Bayesian model from respectively four ERCC1 and ERCC2 cDNA-smMIPs capture replicates is compared with differential expression estimates from respectively 4 ERCC1 and 5 ERCC2 replicates for CaptureSeq (see respectively Supplementary Tables 1 and 2 for statistics).
