Similar studies for GEO DataSets (Select 200043747) - GEO DataSets

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Items: 20

Select item 2000437471.

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(Submitter supplied) Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
17 Samples

Download data: TXT

Series

Accession:: GSE43747

ID:: 200043747

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Select item 2001458812.

Glycolytic body (G body) RIP-sequencing

(Submitter supplied) Glycolytic (G) bodies were purified from hypoxic yeast using differential centrifugation and immunoprecipitation by Pfk2-GFP-Flag in order to determine the RNAs that localize to G bodies by determining the enrichment of RNAs copurified with G bodies over both the flow through and total RNA fractions. We find significant overlap between enriched RNAs and RNAs bound by glycolysis enzymes in normoxic conditions. more...

Organism:: Saccharomyces cerevisiae

Type:: Other

Platform:: GPL17342
6 Samples

Download data: TXT

Series

Accession:: GSE145881

ID:: 200145881

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Select item 2000659923.

Glycolytic Enzymes Bind mRNA and Coalesce in G-bodies Essential for Cell Proliferation Under Hypoxic Conditions

(Submitter supplied) This experiment aimed to identify the direct RNA targets of G-body components Pfk2, Eno1, and Fba1 in budding yeast.

Organism:: Saccharomyces cerevisiae

Type:: Other; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13821
3 Samples

Download data: TXT

Series

Accession:: GSE65992

ID:: 200065992

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Select item 2000488884.

Global signatures of protein binding on structural RNAs in Saccharomyces cerevisiae

(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

Series

Accession:: GSE48888

ID:: 200048888

PubMed Similar studies SRA Run Selector

Select item 2000958515.

Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome

(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

Series

Accession:: GSE95851

ID:: 200095851

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Select item 2000498316.

Differential Protein Occupancy Profiling of the mRNA Transcriptome

(Submitter supplied) Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We have developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing (Baltz and Munschauer et al. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL11154
10 Samples

Download data: BEDGRAPH, TXT

Series

Accession:: GSE49831

ID:: 200049831

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Select item 2001158867.

A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome [Hs]

(Submitter supplied) RBP binding sites were globally mapped by a biochemical technique in human T cells

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: BED, BW

Series

Accession:: GSE115886

ID:: 200115886

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Select item 2000945548.

A global map of RNA binding protein occupancy guides functional dissection of post-transcriptional regulation of the T cell transcriptome [Mm]

(Submitter supplied) RBP binding sites were globally mapped by a biochemical technique in mouse and human T cells

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17021 GPL21103
18 Samples

Download data: BED, BW, CSV

Series

Accession:: GSE94554

ID:: 200094554

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Select item 2000701919.

Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough

(Submitter supplied) Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
13 Samples

Download data: SGR

Series

Accession:: GSE70191

ID:: 200070191

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Select item 20005008610.

The global gene expression pattern by YDR374C deletion

(Submitter supplied) The Ydr374c is the only protein that has the YTH domain in Saccharomyces cerevisiae. The YTH domain was identified by comparing all known protein sequences with the YT521-B splicing factor, and it is found only in eukaryotes. Recently, it has been reported that the YTH domain conveys RNA-binding ability to a new class of proteins. However, the roles of most YTH family members lacking common sequence motifs outside the YTH domain are unknown. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL7293
2 Samples

Download data: TXT

Series

Accession:: GSE50086

ID:: 200050086

Select item 20007327411.

The binding specificity and regulatory effect of WT and redesigned Puf2p

(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

Series

Accession:: GSE73274

ID:: 200073274

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Select item 20007327312.

The binding specificity and regulatory effect of WT and redesigned Puf2p [CLIP-Seq]

(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

Series

Accession:: GSE73273

ID:: 200073273

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Select item 20007322713.

The binding specificity and regulatory effect of WT and redesigned Puf2p [RNA-Seq]

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13821
11 Samples

Download data: TXT

Series

Accession:: GSE73227

ID:: 200073227

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Select item 20001313514.

RBP40_arrays

(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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Series

Accession:: GSE13135

ID:: 200013135

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011038015.

Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale

(Submitter supplied) Many cellular RNAs localize to specific subcellular compartments. Currently, methods to systematically study subcellular RNA localization are limited and lagging behind proteomic approaches. Here, we combined APEX2-mediated proximity biotinylation of proteins with PAR-CLIP to simultaneously profile the proteome and the transcriptome bound by RNA binding proteins in any given subcellular compartment. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
12 Samples

Download data: XLSX

Series

Accession:: GSE110380

ID:: 200110380

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Select item 20011979816.

Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome

(Submitter supplied) RNA-binding proteins (RBPs) play pivotal roles in directing RNA fate and function. Yet the current annotation of RBPs is largely limited to proteins carrying known RNA-binding domains. To systematically reveal dynamic RNA-protein interactions, we surveyed the human proteome by a protein array-based approach and identified 671 proteins with RNA-binding activity. Among these proteins, 525 lack annotated RNA-binding domains and are enriched in transcriptional and epigenetic regulators, metabolic enzymes, and small GTPases. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
3 Samples

Download data: BEDGRAPH

Series

Accession:: GSE119798

ID:: 200119798

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Select item 20005541917.

Coordinating Expression of RNA Binding Proteins with Their mRNA Targets

(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

Series

Accession:: GSE55419

ID:: 200055419

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Select item 20011986718.

Defining the RNA Interactome by Total RNA-Associated Protein Purification

(Submitter supplied) UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae ) and bacteria (E. coli). In all analyses, SILAC labeling was used to quantify protein recovery in the presence and absence of irradiation. more...

Organism:: Saccharomyces cerevisiae

Type:: Other

Platform:: GPL13821
4 Samples

Download data: BEDGRAPH

Series

Accession:: GSE119867

ID:: 200119867

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Select item 20014816619.

Stress-induced translation inhibition through release of 40S scanning initiation factors

(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...