GEO DataSets

(Submitter supplied) To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.; see protocol). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL10418 GPL8306

44 Samples

Download data

(Submitter supplied) BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8546

3 Samples

Download data

(Submitter supplied) The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a key role in discovering these RBPs - most of the known yeast RBPs lack RNA-binding domains that might enable this activity to be predicted. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

4 related Platforms

95 Samples

Download data

(Submitter supplied) In this study, we systematically identified the RNAs associated with a selective sample of 40 of ~600 yeast RNA-binding proteins (RBPs). To identify RNAs associated with each putative RBP, C-terminal tandem affinity purification (TAP)-tagged proteins, expressed under control of their native promoters, were affinity purified from whole cell extracts of cultures grown to mid-log phase in rich medium [1-3]. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

10 related Platforms

153 Samples

Download data

(Submitter supplied) RNA-coimmunopurifications with TAP-tagged Khd1 protein from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control (Gerber et al., 2004). Cells were grown to midlog phase in rich media and harvested by centrifugation. TAP-tagged Khd1 was affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from purified protein samples by phenol-chloroform extraction. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL6419 GPL6420 GPL6421

7 Samples

Download data: PDF

(Submitter supplied) The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL15263

14 Samples

Download data: TXT

(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) 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

Download data

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

Download data

(Submitter supplied) Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL3270 GPL3269 GPL3300

27 Samples

Download data

(Submitter supplied) Three independent experiments: S. cervisiae wild-type (BY4741) and Puf3 mutant cells were grown in minimal medium supplemented with 3% glycerol. Cells were harvested in mid-log phase by centrifugation and total RNA was prepared by hot-phenol extraction. cDNA was prepared with oligo-dT and using a mixture of amino-allyl dUTP and dNTPs, fluorescently labeled (Cy3= wild-type, Cy5 = mutant) and hybridize on S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3300

3 Samples

Download data

(Submitter supplied) RNA-coimmunopurifications with TAP-tagged Puf proteins from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control. Cells were grown to midlog phase and harvested by centrifugation. TAP-tagged Puf proteins were affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input)and from purified protein samples by phenol-chloroform extraction. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL3270 GPL3300 GPL3269

24 Samples

Download data

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

Organism:

Saccharomyces cerevisiae; Neurospora crassa; Neurospora crassa OR74A

Type:

Expression profiling by array

Platforms:

GPL14949 GPL10697

28 Samples

Download data: GPR

(Submitter supplied) Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10697

9 Samples

Download data: GPR

(Submitter supplied) Gene expression profiling was performed to compare RNA abundances in mycelium of Puf knockout strains compared to that in mycelium of wild-type N. crassa

Organism:

Neurospora crassa; Neurospora crassa OR74A

Type:

Expression profiling by array

Platform:

GPL14949

19 Samples

Download data: GPR

(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) Set of experiments done on yeast deletion strains of various non-essential mRNA processing factors. Keywords = splicing Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL105

36 Samples

Download data

(Submitter supplied) Prp4-1 and wt strains were grown at 26°C to A600 of 1.0, then an equal volume of 48°C media was added to bring the temperature to 37°C. Both strains were allowed to grow at 37°C and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature. Keywords = splicing Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL108

12 Samples

Download data

(Submitter supplied) Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL17846

4 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other; Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL9825 GPL17846

16 Samples

Download data: TXT