Databases and Datasets

FAQs

Deletion Strains Available

References

Protocols &Technical Information

Useful Sites & Links

Consortium Members' Addresses

Yeast Deletion Database (consortium members only)

Frequently Asked Questions

  1.  I'm interested in a Deletion strain. What is the best way to get it?
  2.  Can Stanford send me a copy?
  3.  How much do the strains cost?
  4.  How can I buy the whole set?
  5.  What are the genotypes for the strains?
  6.  Is there a complete list of the Deletions made anywhere?
  7.  I'd like to check the sequence of my strain. Is there anyway to get a list of the tag sequences?
  8.  Is there a list of primers anywhere?
  9.  My gene of interest is not on the site. Why not?
10.  Will it ever be made?
11What types of quality control were preformed on the Deletion collection?
12.  What is the criteria of an essential ORF?
13.  Is there a list of the essential ORFs in the collection?
14.  Did anyone look to see whether or not the ORF deletions hit overlapping genes or genes within genes?
15.
Is the background strain S288C?
16. The ftp site for Research Genetics is gone! What on earth is in my microtiter plates?
17. Is there any other way to convey information about the strains that is not on this site for users of the collection?
18. Are there any changes to the collection? i.e., new strains?
19. Is there a way to find out which lab made which strains?

 

I'm interested in a Deletion strain. What is the best way to get it?

First you should see if the strain of interest is available. The searchable web site is no longer working!
We have put all the collection information into text table format here.
Take note of the record number(s)!
Finally, use that number to order the strains from: ATCC, Invitrogen, Open Biosystems or EUROSCARF.

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Can Stanford send me a copy?

Unfortunately not. We have no resources (human or otherwise) that would enable such a monumental task of distributing strains to the scientific community. This is why we contracted with the above distributors for strain distribution.

 

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How much do the strains cost?

All the distributing organizations have reasonable pricing. Please contact the company directly for pricing.

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How can I buy the whole set?

All the distributing organizations are also distributing the collection as "complete" sets by strain background. Please contact the company directly for pricing.

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What are the genotypes for the strains?

BY4730   MATa leu2D0 met15D0 ura3D0
BY4739   MATa leu2D0 lys2D0 ura3D0
BY4741   MATa his3D1 leu2D0 met15D0 ura3D0
BY4742   MATa his3D1 leu2D0 lys2D0 ura3D0
BY4743   MATa/a his3D1/his3D1 leu2D0 /leu2D0 lys2D0/LYS2 MET15/met15D0 ura3D0 /ura3D0 (4741/4742)
homozygous diploids are in the BY4743 background unless 4730/4739 is indicated
can't see the Greek letters?
For more information about the parent strains, check out the reference here.

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Is there a complete list of the deletions made anywhere?

By strain type, check the list of strains_available_by_background.
If you buy a collection set from any of the previously mentioned companies, they should have lists that show what is in their collections.

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I'd like to check the sequence of my strain. Is there anyway to get a list of the tag sequences?

Yes, in the list of strains_available_by_background the UPTAGS and DOWNTAGS are listed along with each ORF. If you would like to check your ORF's tag sequence, there is a tag sequence search page.

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Is there a list of primers anywhere?

Yes. Check out the list of Deletion_primers.

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My gene of interest is not on the site. Why not?

Though the consortium was able to disrupt >95% of all ORFs in SGD up to January 2000, ORFs that were highly similar in sequence (e.g., telomere sequences, highly redundant gene families) were either screened out during the primer picking process, did not integrate uniquely into the genome during the tranformation process or were not in the queue at the time of the project. A list of ORFs not made as deletion strains is available.

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Will it ever be made?

All ORFs that are on the list of ORFs not made were attempted at least two times (many three or four times). Since consortium has finished its efforts these mutants will not be forthcoming. However, we would be greateful to any group that contributes any additional disruption mutants. Please contact the Davis lab.

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What types of quality control were preformed on the deletion collection?

In addition to the PCR confirmation tests, members of the consortium retested Research Genetic's rearrayed strains. Quality control measures include: mating tests, auxotrophic tests, and growth on ethanol/glyerol or G418.
To read a brief description about the QC protocols, click here.

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What is the criteria of an essential ORF?

ORF disruptions that are considered essential were those that were only able to be made in the heterozygous diploid background. Additionally, dissection of tetrads from a heterozygous diploid give segregants as 2 viable : 2 dead. So, essential ORF deletions are only available as heterozygous diploids, while non essential ORF deletions are available as haploids, homozygous diploids and heterozygous diploids.

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Is there a list of the essential ORFs in the collection?

Yes. Check out: Essential_ORFs.

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Did anyone look to see whether or not the ORF deletions hit overlapping genes or genes within genes?

Yes. For a description of the results from such an analysis, see the Overlapping ORFs page.

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Is the background strain S288C?

A conditional yes. The parental background is a derivative of Saccharomyces cerevisiae S288C. For background information about this strain, please refer to the original paper by Brachmann et. al. Click here for abstract.

 

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The ftp site for Research Genetics is gone! What on earth is in my microtiter plates?

Invitrogen bought Research Genetics in 2000 and has recently closed its Huntsville operations, where Research Genetics was located. However, if you need to look at the plate rearray configuration that ResGen used, there is an archive of the last files they had posted here.

 

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Is there any other way to convey information about the strains that is not on this site for users of the collection?

By popular demand, a web based newsgroup has been set up. This is for the yeast community to share information about what they've found in the collection. Postings will not be followed up by the YKO group, which has since been disbanded. To view or add to the posting site, click here. (This will open a new window in your broswer.)

 

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Is there any other way to convey information about the strains that is not on this site for users of the collection?

By popular demand, a web based newsgroup has been set up. This is for the yeast community to share information about what they've found in the collection. Postings will not be followed up by the YKO group, which has since been disbanded. To view or add to the posting site, click here. (This will open a new window in your broswer.)

 

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Are there any changes to the collection? i.e., new strains?

Yes. Please see the YKOv2 page for details.

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Is there a way to find out which lab made which strains?

Sort of. Rather than list each individual lab's strains, I've anonymized the list and given each lab an identifying lab number. The list contains the "borders" of each of the 96 ORFs that the lab attempted to delete: the starting and ending n_record numbers, ORFs and the lab identifier. The list is located here.

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last updated May07. Questions can be sent to: goddess@cmgm.stanford.edu