GEO DataSets

(Submitter supplied) Transcriptome analysis of sus1 mutant in reference to its parental wild type reference. Iterative global median method was used for between sample normalization. z-test was performed to evaluate differential gene expression. Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL772

6 Samples

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(Submitter supplied) Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL220

6 Samples

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(Submitter supplied) Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL220

6 Samples

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(Submitter supplied) Comparison of cDNA from RNA co-IPed with zzYra1 to cDNA from RNA co-IPed with zzMex67 Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL221 GPL220

5 Samples

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(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL220 GPL221

5 Samples

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(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from total RNA; resulting analysis gives Mex67 binding level relative to total abundance for each mRNA Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL221

4 Samples

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(Submitter supplied) Comparison of cDNA from RNA IPed with zzYra1 to that from RNA co-IPed with zz tag alone (control IP) Keywords: equivalent probe

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL220 GPL221

5 Samples

Download data

(Submitter supplied) Comparison of cDNA from RNA IPed with zzMex67 to that from RNA co-IPed with zz tag alone (control IP) Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL220 GPL221

4 Samples

Download data

(Submitter supplied) Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL13821

22 Samples

Download data: NARROWPEAK

(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) Evidence indicates that transcription and mRNA export are linked processes. The molecular mechanisms of this coordination are not clear however. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator and TREX-2 that functions in mRNA biogenesis and export. Here we investigate the coordinated action of SAGA and TREX-2 that is required for gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

32 Samples

Download data: TXT

(Submitter supplied) The nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed and exported. The role of ubiquitylation in this process is increasingly recognized as the ubiquitylation of many key players have been shown to affect mRNA nuclear export. While a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL18340

15 Samples

Download data: BED, GPR

(Submitter supplied) The goal of this experiment is to identify transcripts regulated by Edc3p, an activator of mRNA decapping. Keywords: Genetic modification

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS2625

Platform:

GPL90

10 Samples

Download data: CEL, EXP

Analysis of edc3 null mutant cells. EDC3 encodes an mRNA decapping activator. Results provide insight into the role of Edc3p in mRNA decay.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL90

Series:

GSE6647

10 Samples

Download data: CEL, EXP

(Submitter supplied) Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: TXT

(Submitter supplied) Previous studies suggested that stress-inducible genes are SAGA (Spt-Ada-Gcn5 acetyltransferase)-dominated and characterized by distinct chromatin structures on promoter regions; however, a detailed regulatory mechanism and evolutional advantage of such specialization are not fully understood yet. Here, we newly defined SAGA-regulated genes under direct control of Sgf73p of the deubiquitylating module (DUBm). more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

21 Samples

Download data: BW

(Submitter supplied) RNA binding proteins (RBPs) participate in almost all steps of gene expression, underscoring their potential as key regulators of RNA homeostasis. We structurally and functionally characterized Mip6, a four-RNA Recognition Motif (RRM)-containing RBP, as a functional and physical interactor of the mRNA export factor Mex67. Mip6 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through tryptophan 442 of Mip6-RRM4, whose mutation leads to slow growth of yeast cells in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

4 Samples

Download data: TXT, WIG

(Submitter supplied) The nuclear phase of the gene expression pathway culminates in the export of mature mRNAs to the cytoplasm through nuclear pore complexes (NPCs). GANP (Germinal-centre Associated Nuclear Protein) promotes the transfer to NPCs of mRNAs bound to the transport factor NXF1. Here, we demonstrate that GANP, subunit of the TREX-2 mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

9 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

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

Platforms:

GPL7250 GPL2529

19 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex. We used microarrays to analyze the global impact of THSC/TREX-2 in gene expression and found that Thp1 and Sac3 depletion has a functional impact in highly-expressed, long and G+C-rich genes regardless of their function

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

15 Samples

Download data: CEL