Figure 1

The 3′-bias of transcript abundance can be caused by in vitro transcription (left part) and degradation (right part) of source mRNA. Left part: Specific targets hybridize to the probes along the interrogated transcript with decreasing frequency due to incomplete amplification starting at the primers attached to the 3′-poly-A motif of source mRNA. In contrast, cross-hybridization of non-specific targets is not associated with the 3′-end of the transcripts giving rise to uniform coverage. Right part: Degradation of source mRNA due to RNases from both ends (a and b) and/or fragmentation at randomly chosen positions (c) also result in a 3′-enriched length distribution of amplified RNA giving rise to a similar coverage of the probes as shown in the left part. aRNA fragments are shown in 3′ → 5′ direction (from left to right) in contrast to convention to agree with the probe numbering used (k = 1, 2…) and the intensity decays introduced below