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| Dataset | Description | Keywords | Number of Conditions | Reference |
|---|---|---|---|---|
| 10s oxidative stress | This series represents the rapid response to oxidative stress | stationary phase, oxidative stress, stress | 25 | Aragon AD, et al. (2006) PMID:16507144 |
| 2-Aminobenzimidazole treatment with 5 mM for 2 h | The number and type of synthetic chemicals that are being produced worldwide continues to increase significantly | chemical stimulus, stress | 3 | |
| 300 ppm Citrinin treatment for 2 h (GPL1945) | The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity | chemical stimulus, stress | 6 | Iwahashi H, et al. (2007) PMID:17408496 |
| 300 ppm Citrinin treatment for 2 h (GPL4399) | The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity | chemical stimulus, stress | 9 | Iwahashi H, et al. (2007) PMID:17408496 |
| 30MPa, temp25,16h | Series containes 4 independent experiments and high and low power scanns for each independent experiment | stress | 8 | Iwahashi H, et al. (2005) PMID:15876434 |
| 3′-seq of Saccharomyces cerevisiae grown in eight different conditions | Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) was grown in YPD medium. For control conditions, cells were grown in mid-log phase at 30°C for 20 min or 2 hours. Stress conditions were heat shock (37°C for 20 min), diauxic shift (harvested at 2 hours after glucose depletion), DNA damage (harvested after 2 hours of treatment with 5 µg/ml 4-nitroquinoline 1-oxide (Sigma)). Moreover, four conditions of the yeast metabolic cycle were analyzed. S. cerevisiae strain CEN.PK (MATa URA3 TRP1 LEU2 HIS3 MAL2-8C SUC2) was used and cultivated as described elsewhere (Nocetti and Whitehouse, Genes Dev, 2016). The period of metabolic oscillation was approximately 3.2 h. Cells were harvested at 16, 32, 48, and 60 min from the start of each cycle for one oxidative, two reductive/building, and one reductive/charging phase points. Total RNA from each sample was extracted by the hot phenol method and used for library preparation. 3′-seq libraries were prepared as described previously (Lianoglou et al., Genes Dev, 2013). Each condition was sequenced in three biological replicates. The 27 individual libraries were pooled and subjected to sequencing with HiSeq with SR50 at the Integrated Genomics Operation (MSKCC). | stress | 27 | |
| 50 ppm Patulin treatment for 2 h | Patulin, 4-hydroxy-4H-furo[3,2c]pyran-2(6H)-one, is one of the most popular and characterized mycotoxin observed in agricultural products | stress, chemical stimulus | 6 | Iwahashi Y, et al. (2006) PMID:16506856 |
| A genomic approach highlights common and diverse effects and determinants of susceptibility on the yeast Saccharomyces cerevisiae exposed to distinct antimicrobial peptides | The mechanism of action of antimicrobial peptides (AMPs) was initially correlated with peptide membrane permeation properties | stress | 9 | López-García B, et al. (2010) PMID:21078184 |
| A regulator of RNA Polymerase III at tRNA genes revealed by locus-specific proteome decoding | This SuperSeries is composed of the SubSeries listed below. | stress, RNA processing and metabolism, carbon utilization | 32 | |
| A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters | Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relation-ship between H3K9ac and gene expression remains largely correlative. In this study, we identify a large suite of growth-related genes in yeast that undergo a particularly strong down-regulation of both transcription and H3K9ac upon stress, and delineate the roles of transcriptional activa-tors, repressors, SAGA histone acetyltransferase, and RNA-polymerase II in this response. We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors and activators, that is independent of tran-scription. In response to stress, promoter release of transcriptional activators at growth-related genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of transcriptional re-pressors is required to establish a hypo-acetylated, strongly repressed state. | stress, histone modification | 34 |