Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A universal and cost-effective method for general and specific RNA-protein complex isolation_18S rRNP capture

ABSTRACT: the establishment of a protocol isolating specific RNPs by combining a total RNP isolation with an antisense probe-mediated specific RNP isolation

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Diploid Cell

SUBMITTER: Roosje Van Ende

LAB HEAD: Koen Geuten

PROVIDER: PXD031573 | Pride | 2023-05-10

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	H089026_1p_WNE15_trap25_PRC-5504_1.zip	Other
	H089028_1p_WNE15_trap25_PRC-5504_2.zip	Other
	H089030_1p_WNE15_trap25_PRC-5504_3.zip	Other
	H089032_1p_WNE15_trap25_PRC-5504_4.zip	Other
	H089034_1p_WNE15_trap25_PRC-5504_5.zip	Other

Items per page:

1 - 5 of 12

Publications

A widely applicable and cost-effective method for specific RNA-protein complex isolation.

Balzarini Sam S Van Ende Roosje R Voet Arnout A Geuten Koen K

Scientific reports 20230427 1

Although methodological advances have been made over the past years, a widely applicable, easily scalable and cost-effective procedure that can be routinely used to isolate specific ribonucleoprotein complexes (RNPs) remains elusive. We describe the "Silica-based Acidic Phase Separation (SAPS)-capture" workflow. This versatile method combines previously described techniques in a cost-effective, optimal and widely applicable protocol. The specific RNP isolation procedure is performed on a pre-pur ...[more]

PMID: 37106019

Similar Datasets

A whole-blood RNA transcript based prognostic model in castration-resistant prostate cancer

Project description:Peripheral blood from 62 men with castration resistant prostate cancer was collected between 8/2006 and 6/2008. A panel of 168 inflammation-related and prostate cancer related genes was assessed with quantitative PCR to assess biomarkers predictive of survival. qPCR profiling of whole blood from patients with castration-resistant prostate cancer.

2013-04-02 | E-GEOD-45705 | biostudies-arrayexpress

An rRNA fragment in extracellular vesicles secreted by human airway epithelial cells increases the fluoroquinolone sensitivity of P. aeruginosa

Project description:Extracellular vesicles (EVs) secreted by human airway epithelial cells contain small RNAs that are transferred to P. aeruginosa upon EV exposure. The purpose of this experiment was to characterize the effect of a 27-nucleotide long human 18S rRNA external transcribed spacer fragment on P. aeruginosa protein levels.

2023-10-24 | PXD033165 | Pride

Identification of proteins specifically binding to ac4C RNA probes

Project description:As a newly identified mRNA modification, the regulation of ac4C remains largely unexplored. RNA-binding proteins (RBPs) that specifically binds to ac4C modification and mediate downstream cellular activities (readers) have not been reported yet. We synthesized acetylated and non-acetylated RNA probes by in vitro transcription. The sequences of the probes were segments of FUS and 18s rRNA, which contain ac4C sites as reported. A biotin-RNA pulldown assay and mass spectrometry were performed with HEK 293T cell lysates.

2021-07-20 | PXD027014 | Pride

Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis

Project description:Tuberculosis (TB) is a serious infectious disease, but current methods of detection require improvement in sensitivity, efficiency or specificity. We conducted a microarray experiment, comparing the gene expression profiles in peripheral blood mononuclear cells among individuals with active TB, latent infection, and healthy conditions in a Taiwanese population. These differentially expressed genes may be potential biomarkers that can differentiate between active TB and latent infection. We isolated total RNA from the PBMC from 7 active TB, 7 latent infection, and 7 healthy individuals and profiled their transcriptional profiles to identify signficantly differentially expressed geens that differ among these three groups

2014-10-21 | E-GEOD-62525 | biostudies-arrayexpress

HL-1 mRNA interactome - The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Project description:RNAsfunction as compositionally diverse ribonucleoprotein (RNP) comlplexes, formed through interactions with RNA-binding proteins (RBPs). We explored the murine cardiomyocyte RBP repertoire.

2016-08-17 | PXD002541 | Pride

Pytheas S. cerevisiae 18S rRNA sample analysis

Project description:Mass spectrometry remains an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. This dataset contains the analysis of S. cerevisiae 18S RNA, with identification of pseudouridines through a custom 2H isotopic labeling schema.

2022-05-04 | PXD030563 | Pride

A universal and cost-effective method for general and specific RNA-protein complex isolation_RBPome

Project description:The establishment of a protocol isolating specific RNPs by combining a total RNP isolation with an antisense probe-mediated specific RNP isolation

2023-05-10 | PXD031578 | Pride

Probing Xist RNA structure in cells using Targeted Structure-Seq

Project description:The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.

2016-02-09 | E-GEOD-67667 | biostudies-arrayexpress

LC-MS/MS analysis of human long ribosomal RNA

Project description:The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. Mass spectrometry (MS) enables the identification of modified RNA residues within their sequence contexts, by using analogous approaches to shotgun proteomics. We have developed a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), as part of the OpenMS software framework. NASE allows the reliable identification of (modified) RNA sequences from LC-MS/MS data in a high-throughput fashion. For this validation dataset, we generated samples of human long ribosomal RNA from a cellular extract. The samples were RNase-treated prior to nanoflow LC-MS/MS analysis.

2020-03-31 | PXD016323 | Pride

The transcriptome of TRPV1-positive sensory neurons revealed by subgroup-elimination transcriptomics

Project description:We developed an approach to rapidly eliminate the subgroup of sensory neurons expressing the heat-gated cation channel TRPV1 from dissociated rat sensory ganglia using agonist treatment followed by density centrifugation. To identify transcripts predomintly expressed in TRPV1-positive neurons, we compared the transcriptome of all cells within sensory ganglia versus all cells without TRPV1 expressing neurons using RNA-Seq. Four replicate experiments with RNA from DRG neurons of one rat per experiment were performed. Dissociated neurons were split up in three parts, treated with solvent DMSO (0.1%), casaicin (10 µM), or RTX (100 nM) for 30 min followed by gradient centrifugation. RNA was extracted from the remaining pellet containing either all cells or all cells without TRPV1-positive neurons.

2015-05-12 | E-GEOD-59727 | biostudies-arrayexpress