Advantages of SuperSAGE
The main advantage of SuperSAGE over the preceding techniques SAGE™ and LongSAGE™ is that SuperSAGE (1, 2, patent pending) provides much longer tags with 26 bp instead of the 14 -18 bp quantifiable SAGE™ or LongSAGE™ tags*, respectively.
26 bp tags are 17.000 times more specific than 18 bp quantifiable LongSAGE tags (see table below).
*Due to a bias during ditag formation, LongSAGE tags of 22 bp are not quantifiable (3). However, the 26 bp SuperTAG is fully quantifiable.
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|
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Technique |
Tag-length |
e-value (1) |
Loss of individual tags compared to SuperSAGE (2) |
|
SuperSAGE |
26 bp |
0,00002 |
0 |
|
Long SAGE ™ (not quantifiable) |
21 bp |
0,002 |
13% |
|
Long SAGE ™ (quantifiable) |
18 bp |
0,34 |
17% |
|
SAGE ™ |
14 bp |
128 |
23% |
(1) db: NCBI refseq mRNA nBLAST
(2) data obtained from a mouse SuperSAGE library with a total of 185.191 SuperTAGs and 14.216 individual SuperTAGs.
The 26 bp long SuperTAGs,
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dramatically improve the reliability of tag-to-gene annotation.
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allow amplification of full-length cDNAs from primers designed from the tag sequence by high-stringency PCR using 3’- and 5’-RACE (1) or chromosome walking (4). Thus, SuperSAGE tags can be used for the generation of non-redundant, full-length cDNA libraries.
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can be applied as highly specific probes for the selection of clones in a cDNA or genomic library.
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enable to accurately quantify gene expression in two interacting eukaryotic organisms as e.g. a host and a pathogen (or parasite, or symbiont) during their interaction under natural conditions (1).
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can directly test for gene function via RNA interference (RNAi) or virus-induced gene silencing (VIGS) in high-throughput applications. Here the SuperTag sequence serves as siRNA.
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The long SuperTags are up to 100 times more efficient in gene silencing than conventional 21bp long oligonucleotides and can directly be spotted onto DNA-chips for high-throughput applications. Such SuperTag chips faithfully confirm the SuperSAGE data (5).
Literature cited:
1. Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci USA 100:15718-15723 (2003)
2. Matsumura H, Ito A, Saitoh H, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R. SuperSAGE. Cell Microbiol 7:11-18 (2005)
3. Emmersen J., Heidenblut A., Hřgh A.L., Hahn S., Welinder K.G.and Nielsen K.L. Discarding duplicate ditags in LongSAGE analysis may introduce significant error. BMC Bioinformatics 8:92 doi:10.1186/1471-2105-8-92 (2007)
4. Coemans B, Matsumura H, Terauchi R, Remy S, Swennen R, Sagi L. SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism.Theor Appl Genet.111:1118-26 (2005)
5. Matsumura, H., Nasir, K.H.B., Yoshida K., Ito, A., Kahl, G., Krüger D.H., Terauchi, R. SuperSAGE-array: The direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nature Methods 3: 469-474 (2006)