GEO DataSets

(Submitter supplied) The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combined effect of changes in RNA production, processing, and degradation, and thus, mRNA levels provide an occluded view of transcriptional regulation. To partially disentangle these issues, we carry out genome-wide RNA Polymerase II (“Pol2”) localization profiling in budding yeast in two different stress response time courses. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4131

18 Samples

Download data: GPR

(Submitter supplied) Spt6 is a highly conserved factor that carries out important functions in transcription and chromatin structure. To gain new insights into Spt6, we measured nucleosome occupancy along Saccharomyces cerevisiae chromosome III in an spt6 mutant and found that the level of nucleosomes is greatly reduced accross some but not all coding regions. In addition, genome-wide location analyses of RNA polymerase II showed that the nucleosome loss in the spt6 mutant occurs over highly-transcribed genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4131

8 Samples

Download data: GPR, TIFF

(Submitter supplied) Adaptation of the ChIP-on-chip protocol, to calculate genomic transcription rates in S. cerevisiae. Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL6727 GPL7871

30 Samples

Download data

(Submitter supplied) Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to osmotic stress Keywords: time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4565

35 Samples

Download data

(Submitter supplied) We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique .

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL6727

39 Samples

Download data

(Submitter supplied) Timecourse analyses (0 to 850 min) of exponentially growing BQS252 yeast after shift from YPD to YPGal galactose medium. Total RNA in vivo labeled by run-on, or cDNA labelling using random decamers included. Genomic DNA also examined. Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL772

42 Samples

Download data

(Submitter supplied) The goal of the project was to study the effects on transctiptome of some Rpb1 foot mutations that block Rpb4/7 assembly

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8568

18 Samples

Download data: TXT

(Submitter supplied) In order to maintain the appropriate level of mRNA it is necessary coordinate simultaneously all the steps along the mRNA life cycle. It has been shown that several factors act in the regulation of gene expression as global coordinators. Thus, some kind of information is transferred from the nucleus to the cytoplasm, imprinted in the mRNA. In this way, it is conceivable the existence of mechanisms that ensure the balance between mRNA synthesis and degradation through the information flow from the cytoplasm to the nucleus and vice versa, as a crosstalk among both process to ensure the proper mRNA homeostasis in the cell. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

18 Samples

Download data: TXT

(Submitter supplied) Cells are subjected to dramatic changes on gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. Genome wide localisation studies showed major changes on Pol II localisation towards stress-responsive genes in contrast to housekeeping genes. Pol II relocalisation requires of the Hog1 SAPK, which also associates at stress-responsive loci. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

15 Samples

Download data: BED

(Submitter supplied) Hog1 bypasses stress-mediated downregulation of transcription by PolII redistribution and chromatin remodeling Keyword: genetic modification

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7542

3 Samples

Download data: GPR

(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

Download data

(Submitter supplied) The Saccharomyces cerevisiae MYO1 gene encodes the myosin type II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Deletion of the MYO1 gene prevents actomyosin-driven cytokinesis thereby activating an alternative mechanism that involves the synthesis of a remedial septum. Myo1p deficiency in yeast (myo1) also causes the formation of attached cells, abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, and increased chitin synthesis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL884

6 Samples

Download data: TXT

(Submitter supplied) At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3’-processing of the pre-mRNA and transcription termination. Here we conduct a genome-wide analysis of this 3’-transition in yeast. We find that the 3’-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the poly-adenylation (pA) site and in endonucleolytic RNA cleavage. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL18085 GPL17582 GPL13272

44 Samples

Download data: BED, TXT

(Submitter supplied) RNA Polymerase II was mapped over 4% of the yeast genome by ChIP, in wild-type and a handful of mutants in transcriptional termination factors. Keywords: ChIP-chip, transcription termination

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL1950

9 Samples

Download data

(Submitter supplied) In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprograming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II (Pol II) and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV-crosslinking immediately following glucose withdrawal (0, 4, and 8 minutes). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

24 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platforms:

GPL7662 GPL8546

60 Samples

Download data

(Submitter supplied) In this study, we systematically identified RNAs associated with ribosomes. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a or Rpl16b, expressed under control of thier native promoter, were affinity purified from whole cell extracts of cultures grown to mid-log phase in minimal medium. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL8546

8 Samples

Download data

(Submitter supplied) In this study, we systematically identified ribosome associated RNAs. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a, expressed under control of its native promoter, was affinity purified from whole cell extracts of cultures grown to mid-log phase. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL7662

52 Samples

Download data

(Submitter supplied) Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4613

12 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) Background: As carbon sources are exhausted, Saccharomyces cerevisiae cells exhibit reduced metabolic activity and cultures enter stationary phase. We asked whether cells in stationary-phase cultures respond to additional stress at the level of transcript abundance. Results: Microarrays were used to quantify changes in transcript abundance in cells from stationary-phase cultures. In response to oxidative stress, more than 800 mRNAs increased within 1 minute. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL1859 GPL3153

219 Samples

Download data: TIFF