Figure 1

SAGE tag primer development. SAGE tag pools are put through various filtrations to produce a source of SAGE tag primers that are used in STACE experiments. 1) SAGE tag libraries are downloaded from the MultiSAGE website. 2) All SAGE tags that do not fully map to the genome as one single uninterrupted alignment are discarded. 3) SAGE tags that map to annotated transcribed sequences are discarded. 4) SAGE tags that have a low level of expression and are possible errors in sequencing are discarded. 5) SAGE tags that are found to overlap with intronic sequences or map near a 5' or 3' boundary are eliminated. 6) Only tags with GC content between 35% and 45% are retained. 7) SAGE tags are edited into primer form. All SAGE tags that are likely to produce secondary structure (i.e. hairpins, homo-dimers, hetero-dimers) are discarded. 8) A final list of SAGE tag primers is procured.