Figure 3

Comparison of tag sequences in three MPSS libraries produced from the same RNA sample. A. The three libraries were sampled to various sizes in a step-wise fashion to examine the effect of library size on the number of distinct tag sequences identified (as done for single SAGE and MPSS libraries in Fig. 1). Closed diamonds represent random sampling of tags from all three libraries combined. Open diamonds represent sampling of each library in turn. Clearly, although the number of distinct species identified by each library (with the possible exception of the third) appears to approach saturation, each library is sampling a different subset of sequences from the initial RNA pool. B. Venn diagrams showing the distribution of tag sequences between the three MPSS libraries. The library represented by the blue circle is the one used in most of the analyses presented in this study. Diagram (i) represents all the different tag sequences in the libraries. Diagram (ii) represents only those tags that match the genome; this reduces the influence of sequencing errors. In both comparisons, the majority of distinct sequences are found in only one library. Diagram (iii) represents known transcripts in the UTBS dataset found expressed in the sense direction. Here the pattern is less marked, but still only half the transcripts were observed in all three libraries (1,312/2,646). The improvement in the correlation of the libraries for known transcripts (i.e. those in the UTBS) was expected because more highly expressed transcripts are more likely to have been previously identified, and therefore known transcripts tend to be more abundant and have a greater chance of being sampled.