Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA234034 | ENA |
REPOSITORIES: ENA
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Project description:We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification). Nonsense mediated mRNA decay (NMD) of these mRNA reporters was tested by using Agilent barcode microarrays by taking advantage of molecular barcodes introduced just downstream the stop codon during strain construction. We introduced in each DAmP strain either a neutral mutation (deletion of YEL068C) or the deletion of essential factors for NMD: NAM7 and NMD2. The resulting haploid cells were tested for changes in DAmP mRNA levels by comparing an RNA sample with a DNA genomic sample. Differences between the samples indicate the sensibility of the DAmP mRNAs to degradation through NMD. The large scale results were validated by Q-PCR analysis of individual strains. A strong negative correlation between the level of destabilization elicited by a long 3' UTR and the size of the coding sequence suggests that long ORF mRNAs can escape NMD even in the presence of a long 3' UTR. Three samples were analysed and for each sample a technical replicate was performed, starting from the raw cellular material. YEL068C samples represent the reference population while NMD2 and NAM7 samples are the ones important for the analysis. Only a very limited part of the Agilent barcode microarray signal (barcodes corresponding to the “up” tag in the DamP strain) was used for the interpretation of the data.
2014-01-10 | E-GEOD-53954 | biostudies-arrayexpress
Project description:We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification). Nonsense mediated mRNA decay (NMD) of these mRNA reporters was tested by using Agilent barcode microarrays by taking advantage of molecular barcodes introduced just downstream the stop codon during strain construction. We introduced in each DAmP strain either a neutral mutation (deletion of YEL068C) or the deletion of essential factors for NMD: NAM7 and NMD2. The resulting haploid cells were tested for changes in DAmP mRNA levels by comparing an RNA sample with a DNA genomic sample. Differences between the samples indicate the sensibility of the DAmP mRNAs to degradation through NMD. The large scale results were validated by Q-PCR analysis of individual strains. A strong negative correlation between the level of destabilization elicited by a long 3' UTR and the size of the coding sequence suggests that long ORF mRNAs can escape NMD even in the presence of a long 3' UTR.
2014-01-10 | GSE53954 | GEO
Project description:Growth assay in the presence of a toxic chemical (sr7575) that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.
2015-12-09 | GSE60934 | GEO
Project description:The ability to perform complex bioassays in parallel enables experiments otherwise impossible due to throughput and cost constraints. By way of example, highly parallel chemical-genetic screens using pooled collections of thousands of defined Saccharomyces cerevisiae gene deletion strains are feasible because each strain is barcoded with unique DNA sequences. It is, however, time consuming and expensive to individually barcode individual strains. To provide a simple and general method of barcoding yeast collections, we built a set of donor strains, called Barcoders, with unique barcodes that can be systematically transferred to any S. cerevisiae collection. We applied this technology by generating a collection of barcoded DAmP (Decreased Abundance by mRNA Perturbation) loss-of-function strains comprising 87.1% of all essential yeast genes. This test collection validates both the Barcoders and the DAmP collection as useful tools for genome-wide chemical genetic assays.
2008-07-03 | E-MEXP-1671 | biostudies-arrayexpress
Project description:Growth assay in the presence of Selenomethionine that uses the barcoded collections of yeast gene modification (deletion or DamP) to identify strains that are hypersensitive to the presence of the aminoacid.
2017-03-17 | GSE84340 | GEO
Project description:Growth assay in the presence of a toxic chemical that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.
2019-12-31 | GSE125353 | GEO
Project description:Saccharomyces cerevisiae deletion and DAmP collections chemogenomic screen with Selenomethionine
| PRJNA328936 | ENA
Project description:Transcription profile of pho85 damp strain during growth in no phosphate medium
| PRJNA261792 | ENA
Project description:Transcription profile of phm3 damp strain during growth in no phosphate medium
| PRJNA261794 | ENA