Set1, H3K4A, set1htz1, set1htz1sir2 transcription profiles
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE4826 | GEO | 2006/05/17
SECONDARY ACCESSION(S): PRJNA95637
REPOSITORIES: GEO
Similar Datasets
Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type Keywords: quadruplicate mutant:WT analysis, with dye-swapping
2006-06-01 | GSE4934 | GEO
Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type mutant and wild-type grown to log phase, YPAD, 30C, purified mRNA, reverse-transcribed to cDNA, labelled with Cy5/Cy3, hybridized to whole genome ORF microarrays
2010-06-11 | E-GEOD-4826 | biostudies-arrayexpress
Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in bre1 compared to wild-type. Arrays done in quadruplicate with dye-swaps.
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Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in bre1 compared to wild-type.
2009-11-19 | GSE13701 | GEO
Project description:Purpose: Understand the synergistic relationship between the methyltransferases Set1 and Set5 in the regulation of gene expression. Methods: Total mRNA was obtained from two independent biological replicates each of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ S. cerevisiae strains. Libraries were generated and sequenced using an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were mapped using TopHat and expression levels were quantified using Cufflinks. Results: We generated FPKM expression values for each transcript and identified the differentially expressed genes using an FDR-adjusted p-value of 0.05. Subsequent data analysis was restricted to genes with fold-change greater than 1.7 relative to WT. Our results show that Set1 and Set5 have roles primarily in transcription repression. Moreover, lack of both Set1 and Set5 results in a synergistic exhacerbation of the transcriptional derepression observed in the single mutants. Further analysis revealed a specific enrichment of the Set5/Set1-repressed genes near repetitive DNA sequences of the genome. Conclusions: Our study uncovers an unexpected synergistic role of Set1 and Set5 in transcription repression of telomeric regions and Ty retrotransposons.
2014-01-15 | GSE52086 | GEO
Project description:Purpose: Understand the synergistic relationship between the methyltransferases Set1 and Set5 in the regulation of gene expression. Methods: Total mRNA was obtained from two independent biological replicates each of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ S. cerevisiae strains. Libraries were generated and sequenced using an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were mapped using TopHat and expression levels were quantified using Cufflinks. Results: We generated FPKM expression values for each transcript and identified the differentially expressed genes using an FDR-adjusted p-value of 0.05. Subsequent data analysis was restricted to genes with fold-change greater than 1.7 relative to WT. Our results show that Set1 and Set5 have roles primarily in transcription repression. Moreover, lack of both Set1 and Set5 results in a synergistic exhacerbation of the transcriptional derepression observed in the single mutants. Further analysis revealed a specific enrichment of the Set5/Set1-repressed genes near repetitive DNA sequences of the genome. Conclusions: Our study uncovers an unexpected synergistic role of Set1 and Set5 in transcription repression of telomeric regions and Ty retrotransposons. mRNA profiles of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ were generated by sequencing using an Illumina HiSeq2000 platform. Two biological replicates of each strain were used.
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Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Saccharomyces cerevisiae S288c was grown on two different media and two different primers were used for reverse transcription: oligo(dT) and Multi-Targeted Primer [MTP] protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2). Two biological replicates and dye swapping
2010-07-20 | E-GEOD-22992 | biostudies-arrayexpress
Project description:The intracellular metabolome of S. cerevisiae mutants in the gene AYT1 were measured under glucose growth conditions, as well as growth on oleate.
2021-01-27 | MSV000086772 | MassIVE
Project description:A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and my provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well understood model eukaryote, we still do not have a full catalog and understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the aim of increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify and map the locations of unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells, revealing 540 currently unannotated, presumably low abundance or short-lived RNAs, of which 231 are previously unknown and unique to this study. It is likely that many of these represent cryptic unstable transcripts (CUTs) which are rapidly degraded and whose function(s) within the cell are still unclear, while others may represent novel functional transcripts. Of the 271 transcripts we identified in current intergenic regions, greater than 90 percent have lower conservation scores amongst closely related yeast species than 95 percent of the verified ORFs in S. cerevisiae; such regions of the genome have typically been less well studied, and by definition encode transcripts that distinguish S. cerevisiae from these closely related species. Keywords: Saccharomyces cerevisiae, transcriptome, salt shock, xrn1, rrp6, lsm1, pat1, RNA degradation
2008-12-18 | GSE11800 | GEO
Project description:The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavours, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well documented that codon usage can affect translation, and most likely mRNA stability in eukaryotes, remarkably few quantitative studies explore the impact of watermarking on transcription, protein expression and physiology in the popular model and industrial yeast Saccharomyces cerevisiae. The present study, using S. cerevisiae as eukaryotic paradigm, designed, implemented and experimentally validated a systematic strategy to watermark DNA with minimal alteration of yeast physiology. The thirteen genes encoding proteins involved in the major pathway for sugar utilization (i.e glycolysis and alcoholic fermentation) were simultaneously watermarked in a yeast strain using the previously published pathway swapping strategy. Carefully swapping codons of these naturally codon optimized, highly expressed genes, did not alter transcript abundance, protein activity and yeast physiology. The markerQuant bioinformatics method could reliably discriminate native from watermarked genes and transcripts. Furthermore, presence of watermarks enabled selective CRISPR/Cas genome editing, specifically targeting the native gene copy while leaving the synthetic, watermarked variant intact. This study offers a validated strategy to simply watermark genes in S. cerevisiae.
2020-06-29 | GSE135470 | GEO