GEO DataSets

(Submitter supplied) Identifying transcripts that are associated with the post transcriptional regulator Vts1 in yeast by co-immuno precipitation. Keywords: RNA pulldown, Co-IP

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL3230 GPL3229

4 Samples

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(Submitter supplied) The experiment was designed to look for genes up/downregulated in the absense of Vts1p compared to wild-type cells grown in steady state conditions. Keywords: VTS1

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1644

Platform:

GPL90

5 Samples

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Analysis of a strain lacking Vts1p. Vts1p is a putative post-transcriptional regulator that uses a sterile alpha motif (SAM) domain to bind an RNA hairpin termed the Smaug recognition element (SRE). Results identify genes that may be regulated by Vts1p and contain one or more copies of the SRE.

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL90

Series:

GSE3859

5 Samples

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(Submitter supplied) Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellelar functions and dynamics upon changing environmental condictions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

10 Samples

Download data: BED

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

23 Samples

Download data: TXT

(Submitter supplied) PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

12 Samples

Download data: TXT

(Submitter supplied) PUF proteins have become a leading scaffold for designing RNA-binding proteins to contact and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time. We show, by HITS-CLIP and PAR-CLIP, that S. cerevisiae Puf2p, a non-canonical PUF protein, binds more than 1000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

11 Samples

Download data: TXT

(Submitter supplied) Purpose: High-throughput sequencing has transformed modern biology, but its repertoire is currently confined to reading DNA molecules. Here, we report hardware and software adaptations that allow the very methods that enabled the genomic sequencing revolution to be applied to fluorescence-based biochemical assays, on a massive scale. Methods: Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17143

1 Sample

Download data: FASTQ, TXT, XLSX

(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

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(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

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(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

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(Submitter supplied) Expanding the binding specificity for RNA recognition by a PUF domain

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

9 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional regulation by RNA binding proteins (RBPs) plays prominent roles in a variety of biological processes. In this study, by analyzing the global regulatory relationship between RBPs and their target mRNAs in yeast, we discovered that most RBP genes are co-regulated with their target genes, but the RBPs tend to dampen expression variation among their target mRNAs. We further examined a well-studied RBP gene, PUF3, and found that the protein decreases the variation of its target mRNAs by differentially affecting their decay. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: BED

(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

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(Submitter supplied) PAPD5 is one of the seven members of non-canonical poly(A) polymerases in human cells. There are previous reports about polyadenylation dependent degradation of pre-ribosomal RNAs and uridylation dependent degradation of histone mRNAs in vivo. In this study, we observed polyadenylation but not polyuridylation activity of PAPD5 with in vitro assays. We aimed to get genome-wide targets of PAPD5 and used PAR-CLIP and deep sequencing for this purpose.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: TXT

(Submitter supplied) We quantified the exact RNA binding sites of the Ssd1 protein in Saccharomyces cerevisiae, in exponential growth and heat shock conditions, using the CRAC protocol. We used a His-TEV-protein A tag (HTP) on the C-terminal of the genomic copy of Ssd1, with the 3'UTR replaced by the 3'UTR/terminator from the K. lactis Ssd1 homolog, followed by a KlURA3 selection marker.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Other

Platform:

GPL29267

5 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome, without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA-association. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

74 Samples

Download data: BEDGRAPH, TXT