Protocols &Technical Information
Dear Colleagues,
Welcome to the Saccharomyces Genome Deletion Project web page.
The purpose of this page is to communicate protocols, methods and information
about the project. Please let us know what information you would like
to see included or suggest useful links.
Project Overview
In 1996 the Saccharomyces Genome Project has revealed the presence of more than 6000 open reading frames (ORFs) in the S. cerevisiae genome. Approximately one third of these ORFs had no known function four years after their discovery. The goal of the Saccharomyces Genome Deletion Project was to generate as complete a set as possible of yeast deletion strains with the overall goal of assigning function to the ORFs through phenotypic analysis of the mutants.
The method used was a PCR-based gene deletion strategy to generate a start- to stop- codon deletion of each of the ORFs in the yeast genome. As part of the deletion process, each gene disruption was replaced with a KanMX module and uniquely tagged with one or two 20mer sequence(s) . The presence of the tags can be detected via hybridization to a high-density oligonucleotide array, enabling growth phenotypes of individual strains to be analyzed in parallel .
Four different mutant collections were generated: haploids of both mating types, homozygous diploids for non-essential genes, and heterozygous diploids, which contain the essential and non essential ORFs. Our results show that 18.2% of the genes are essential for growth on rich gluose media and approximately 15% of the homozygous diploid disruptions cause slow growth in this type of media.
When the Yeast Knock-out (YKO) deletion collection was released in 2000, the deletion strains were based on the annotation of the available yeast genome sequence. Since the initial release of the collection the yeast genome has undergone numerous annotation changes. The YKOv2 (Yeast Knock-Out version2) supplemental set is the result of two labs’ efforts to update the existing collection.
To date, the Saccharomyces Genome Deletion Project consortium disrupted 90% of the yeast genome. By ORF class: 92% verified, 88% uncharacterized and 65% dubious ORFs have been deleted. At least 10% of the yeast genome is redundant. Highly simliar ORFs in gene families were difficult to chose primers for, so many of these were unsucessful deletion attempts. (To check out what wasn't deleted, check here.)
More than 20,000 strains are currently available.
last updated May07 - questions or comments should be addressed to: Corey Nislow