GEO DataSets

(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) The goal of the project was to study synthesis rates (SR) and mRNA levels (RA) genome wide in a series of aneuploid strains to check for the posible variation in SR and RA in the genes of the aneuploid chromosome withe regard to the rest of the genome. We used Genomic Run-On (GRO) experiment to mesaure SR and RA values.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24366

24 Samples

Download data: TXT

(Submitter supplied) Understanding chromatin dynamics is a key to other related processes, including DNA replication, transcription and recombination. As a first step, recently, an increasing amount of effort has been devoted to precisely define nucleosome positioning in different organisms. The most popular method to do so is digestion by Micrococcal nuclease (MNase), nowadays followed by ultrasequencing of the generated fragments. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL13272

3 Samples

Download data: BED

(Submitter supplied) We analysed the transcriptomic signature associated to fast and slow growing microcolonies generated after the encapsulation of single cells belonging to a clonal wild-type population, in alginate microspheres. This allowed us to identify particular gene expression signatures associated to each subpopulation. In particular, we found that slow growing cells display an increased expression of respiratory genes even when growing in glucose rich media.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

16 Samples

Download data: TXT

(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) The goal of the project was to check the effect on transcription rate of a sudden depletion of Mex67 protein by using a thermosensitive mutant: mex67-5

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8568

6 Samples

Download data: TXT

(Submitter supplied) The goal of the project was to check the differential effect on transcription rate of a sudden degron-induced depletion of Hpr1 protein and its comparison towards the effect of a constitutive absence of Hpr1 protein in a deletion strain.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13619

6 Samples

Download data: TXT

(Submitter supplied) We analyzed the effect of SPT16 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a thermosensitive spt16 point mutant (G132D) mutant at 35 ºC comparing with permisive temperature (30 ºC) and a wt treated in the same way.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13619

12 Samples

Download data: TXT

(Submitter supplied) We analyzed the effect of SAC3, SUS1 and SRC1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants and the partial C-truncated version of Sac3 comparing with a wild type. Some data for mRNA amounts (sus1 ans src1 mutants) are not included because were already in GEO database: GSE920 and GSE6370 accession numbers.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL4565 GPL8568

9 Samples

Download data: TXT

(Submitter supplied) We analyzed the effect of PUB1 and NGR1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants comparing with a wild type in both glucose (YPD) and galactose (YPGal) media. Some data for the wt in YPGal are not included because were already in GEO database: GSE1002 accession number.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL6727

8 Samples

Download data: TXT

(Submitter supplied) We have developed a new genome-wide protocol for nascent transcription analysis at high resolution in the yeast Saccharomyces cerevisiae. This protocol is based in run-on labeling of nascent RNA with a biotinylated precursor. We call it BioGRO for biotin-based genomic run-on.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL18871

7 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

9 Samples

Download data: TXT

(Submitter supplied) GRO (Genomic run-on) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: Genomic run-on GRO

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL6727 GPL8568

17 Samples

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(Submitter supplied) RPCC (RNA pol II ChIP-on-chip) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: ChIP-chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platforms:

GPL8568 GPL6727

20 Samples

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(Submitter supplied) mRNA amount (RA) analysis of W303 hog1 mutant 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

21 Samples

Download data

(Submitter supplied) Transcription rate (TR) analysis of W303 hog1 mutant 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

21 Samples

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(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

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(Submitter supplied) Gene expression analysis of a src1 yeast strain mutant and wt yeast strain growing in exponential phase in YPD Keywords: genetic modification

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4565

9 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

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(Submitter supplied) Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that are activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL13304 GPL17275

64 Samples

Download data: BEDGRAPH