GEO DataSets

Culture synchronized by elutriation and samples removed at several time points up to 6.5 h. Included as part of a comprehensive identification of cell cycle-regulated genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 14 time sets

Platform:

GPL59

Series:

GSE24

14 Samples

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(Submitter supplied) Yeast cells were arrested either in G1 (for CLN3 overexpression) or in G2/M (for CLB2 overexpression). The cyclin was then induced, and samples were taken. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS110

Platform:

GPL61

3 Samples

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(Submitter supplied) Small G1 daughter yeast cells were isolated by centrifugal elutriation. They were then released into YEP ethanol, and followed through one cell cycle, with samples being taken every 30 minutes. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS39

Platform:

GPL59

14 Samples

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(Submitter supplied) Yeast cells were blocked in telophase using a cdc15-2 temperature senstive mutant at restrictive temperature. The culture was then shifted to permissive temperature (25oC), and released into the cell cycle. Samples were then taken during the course of almost three full cell cycles. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL62

25 Samples

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(Submitter supplied) These data are from a time series, where yeast were arrested in alpha-factor, then the alpha-factor was washed out, and the cells were release into fresh medium. Samples were taken every 7 minutes as the cells went through the cell cycle. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS38

Platforms:

GPL59 GPL60

18 Samples

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Cells arrested in G1 for CLN3 overexpression. Included as part of a comprehensive identification of cell cycle-regulated genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 time sets

Platform:

GPL61

Series:

GSE25

2 Samples

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Culture synchronized by alpha factor arrest, then samples taken every 7 minutes as cells went through cell cycle. Included as part of a comprehensive identification of cell cycle-regulated genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 16 time sets

Platform:

GPL59

Series:

GSE22

16 Samples

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(Submitter supplied) The wild-type (grown on galactose or glucose) or msn2/4 mutant (grown on galactose) strains were grown aerobically. At time zero (generation 0) the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth. Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS2002 GDS2003

Platform:

GPL1535

45 Samples

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Analysis of catabolite-derepressed (galactose) wildtype JM43 and isogenic msn2/4 mutant KKY8 cells shifted to short-term anaerobiosis (2 generations). Msn2 and 4 are key stress factors. Results suggest Msn2/4 involvement in metabolic remodeling during acclimatization to short-term anaerobiosis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 genotype/variation, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

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Analysis of catabolite-repressed (glucose) or derepressed (galactose) wildtype JM43 cells shifted from aerobiosis to anaerobiosis (2 generations). Results identify metabolic remodeling that occurs during acclimatization to short-term anaerobiosis in galactose but not in glucose.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 growth protocol, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

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(Submitter supplied) DNA topoisomerase-2 and high mobility group protein Hmo1 are known to regulate chromatin architecture by regulating gene boundaries. Here we report how these proteins affect global RNA level after inactivation of Top2 and Hmo1. Our data indicate that inactivating Hmo1 has a drastic effect on transcription levels of 20% yeast genes, however, this phenomenon can slightly be rescued by inactivating Top2 functions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17143 GPL18249

18 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) DNA topoisomerases assist DNA replication & transcription events by controlling supercoiling alterations. We investigated supercoil distribution across the yeast genome and compared with the accumulation of RNA pol2 and DNA topoisomerases particularly in S-phase. Our data indicate that Top2 along with Hmo1 maintain negative supercoil at gene boundaries by stabilizing alternative DNA structures. To understand how DNA superhelical tension accumulates across the genome we have adopted previously described method [Naughton C et al., 2013] to budding yeast where a biotin molecule was attached to TMP via a linker (bTMP). more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

68 Samples

Download data: BED, BEDGRAPH, CEL

(Submitter supplied) Measurement of expression levels as a time course after shifting temperature-sensitive splicing factor mutant cells from 23C to 37C. Analysis of WT SS330, prp17 null, prp17-1 and prp22-1 cells. Samples were analyzed at 0, 5, 15, 30, 60 and 120 min. Keywords = pre-mRNA splicing Keywords = time course Keywords = intron Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS759

Platform:

GPL1458

24 Samples

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Analysis of gene expression in temperature sensitive pre-mRNA splicing factor mutants prp17 null, prp17-1, and prp22-1 at various time points following a shift from the permissive temperature of 23°C to the restrictive temperature of 37°C. Results identify substrates of Prp17p and Prp22p.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 4 genotype/variation, 2 temperature, 6 time sets

Platform:

GPL1458

Series:

GSE1784

24 Samples

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(Submitter supplied) The complete set of open reading frames of the S. cerevisiae genome were obtained from Research Genetics (Huntsville, Ala.) and amplified by PCR Protocol: Refer to Townsend, Cavalieri and Hartl 2003

Organism:

Saccharomyces cerevisiae

3 Series

95 Samples

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(Submitter supplied) S. cerevisiae Y440 Mat a leu2 was grown in YEPD at 28 degrees C with aeration to exponential growth phase and was subjected to a hydrostatic pressure of 50 and 200 MPa for 30 minutes at room temperature. Total RNA was extracted using phenol/chloroform and further precipitated with 3 M sodium acetate / absolute ethanol. Extracted RNA samples were treated for 10 min with 0.5 U of RNAse-free DNAse I / ]g RNA at 37 oC to remove any residual genomic DNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2658

2 Samples

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(Submitter supplied) Microarray analysis was used to identify all cryptic promoters in the S. cerevisiae genome that are activated in spt6 and spt16 mutants. These experiments showed that cryptic initiation is widespread, occurring in approximately 1,000 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7078

6 Samples

Download data: GPR

(Submitter supplied) E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2552

12 Samples

Download data: TIFF, TXT

(Submitter supplied) E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2549

10 Samples

Download data: TIFF, TXT

(Submitter supplied) We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors 1 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3292

35 Samples

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