Why are the tag sequences in the chip file backwards from those listed at the Saccharomyces Genome Deletion Project webpage?
The Affymetrix convention is to list sequences 3'→5' because that is how they are synthesized on the array. The Saccharomyces Genome Deletion Project webpage lists the sequences 5'→3'. These are available in their "downloads" section: http://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.html.
What are the mixed oligos (aka "soaking primers") for?
| Without the mixed oligos, tags stick together by their common primer sequences. This can interfere with hybridization. |
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| Oligos complimentary to the common primers are added in excess to make the tag sequences more accessible for hybridization. |
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There are 8 oligos in the mix -- the forward and reverse primer for the uptag, the forward and reverse primer for the downtag, and the complements of these four. All of the mixed oligos are unbiotinylated.
How many tags are there on the array?
There are 15,476 different tags.
15452 of them have 5 replicate features on the array.
24 have 55 replicate features.
11876 are in use by the yeast deletion collection.
3600 are currently unused.
I would like to develop a new use for the TAG4 array that will only use some of the tags. Can you give me a list of tags that have worked well in your experiments?
If you are designing an application that only uses a subset of the tags, and you can afford to be choosy, you may prefer to pick those that have performed well in yeast because these tags may be more likely to be free of problems when used in other systems (such as unexpected problems with PCR amplification). An ordered list of tag quality in our experiments is provided in the Downloads section.
If you are planning an application that will use almost all of the tags, don't worry! Tags that don't work well in yeast deletion experiments could be performing poorly for many reasons, most of which have nothing to do with the tag sequence, so these tag sequences are not necessarily bad to use in other applications. The majority of tags that perform poorly in yeast are likely caused by the strain, not by an inherent problem with the tag sequence.