Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RIp-chip experiments with the Scw1, Zfs1 and Red1 RNA-binding proteins

ABSTRACT: We have used RIp-chip to identify mRNAs that coprecipitae with specific RNA-binding proteins

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Juan Mata

PROVIDER: E-MTAB-2709 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RIp-chip experiments with proteins that do not contain RNA-binding domains

Project description:In order to assess the prevalence of cotranslational assembly of protein complexes we performed RIp-chip experiments with many proteins that do not conatin RNA-binding motifs

2012-05-20 | E-TABM-1158 | biostudies-arrayexpress

RIp-chip experiments with the Scw1 RNA-binding protein on ageing samples

Project description:We have used RIp-chip to identify mRNAs that coprecipitate with specific Scw1 RNA-binding protein on ageing samples

2019-06-01 | E-MTAB-7618 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (II)

Project description:RIP-chip experiments to identify RNAs associated with components of the Ccr4-Not complex in fission yeast

2015-09-25 | E-MTAB-3057 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (III)

Project description:RIP-chip experiments to identify RNAs associated with the Mmi1 protein in fission yeast

2015-09-25 | E-MTAB-3058 | biostudies-arrayexpress

Role of the Ccr4/Not complex in the regulation of heterochromatin in Schizosaccharomyces pombe (VI)

Project description:RIP-chip experiments to identify RNAs associated with components of the Ccr4-Not complex in fission yeast

2015-09-25 | E-MTAB-3065 | biostudies-arrayexpress

RIp-chip experiements with the Exo2 and Eti1 proteins

Project description:We have used RIp-chip to identify mRNAs that coprecipitae with specific proteins, and later used the protein RNA interactions to predict protein-protein associations. To test whether some of the interactions we see require intact polysomes (that is, ribosomes translating mRNAs) we treated the extracts (and, in some cases, also the cells) with different compounds. In this case, we have a standard protocol, one in which the buffers contain EDTA, and one in which it includes puromycin.

2014-05-05 | E-MTAB-1856 | biostudies-arrayexpress

Ribonucleoprotein immunoprecipitation of Schizosaccharomyces pombe cells using the RNA-binding protein Meu5

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the RNA-binding protein Meu5 from the fission Schizosaccaromyces pombe

2011-01-01 | E-TABM-932 | biostudies-arrayexpress

RNP immunoprecipitation of fission yeast using Rng3p myosin-specific chaperones to investigate if the association of Rng3p with RNAs occurs on ribosomes

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the Rng3p myosin-specific chaperones from the fission Schizosaccaromyces pombe. Rng3p associates with RNAs encoding myosins. To investigate if the association of Rng3p with these RNAs occurs on ribosomes, Rng3-purified fractions were immunoprecipitated with antibodies against a ribosomal RNA or an unrelated antibody. The RNAs present in the second immunoprecipitate were analysed using DNA microarrays

2008-12-23 | E-TABM-564 | biostudies-arrayexpress

Transcription profiling by array of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

Project description:BACKGROUND: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. RESULTS: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. CONCLUSIONS: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-143]

2013-04-24 | E-BUGS-143 | biostudies-arrayexpress

Ribonucleoprotein immunoprecipitation of fission yeast to study myosin proteins and myosin-specific chaperones

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using various myosin proteins and myosin-specific chaperones from the fission Schizosaccaromyces pombe. Two strains were used. In rng3TAP the rng3 protein has been tagged with TAP to allow its detection and immunoprecipitation. The TAP strain expresses the TAP sequence alone (without being attached to an other protein)

2008-12-23 | E-TABM-516 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data