Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 2

ABSTRACT: The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Animal Cap, Early Embryonic Cell

SUBMITTER: Kevin Drew

LAB HEAD: Edward Marcotte

PROVIDER: PXD017650 | Pride | 2020-03-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	xl_animalcaps_SEC_Control_09a_20191004..comet.pep.xml	Pepxml
	xl_animalcaps_SEC_Control_09a_20191004.MSGF+.pride.mztab.gz	Mztab
	xl_animalcaps_SEC_Control_09a_20191004.MSGF.mzid.gz	Mzid
	xl_animalcaps_SEC_Control_09a_20191004.mzXML	Mzxml
	xl_animalcaps_SEC_Control_09a_20191004.prot_count_mFDRpsm001.group	Other

Items per page:

1 - 5 of 918

Publications

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.

Drew Kevin K Lee Chanjae C Cox Rachael M RM Dang Vy V Devitt Caitlin C CC McWhite Claire D CD Papoulas Ophelia O Huizar Ryan L RL Marcotte Edward M EM Wallingford John B JB

Developmental biology 20200906 1-2

Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application ...[more]

PMID: 32898505

Similar Datasets

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 1

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

2020-03-10 | PXD017659 | Pride

Systematic discovery of endogenous ribonucleoprotein complexes - RNA DIF-FRAC Human HEK293T Cells Replicate2

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Human HEK293T with and without RNAse A treatment.

2019-10-25 | PXD014820 | Pride

Systematic discovery of endogenous ribonucleoprotein complexes - RNA DIF-FRAC Human HEK293T Cells Replicate1

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Human HEK293T with and without RNAse A treatment.

2019-10-18 | PXD015406 | Pride

Widespread RNA Binding by Chromatin Associated Proteins

Project description:Recent evidence suggests that RNA interaction can regulate the activity and localization of DNA binding proteins, particularly chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Here, we introduce formaldehyde RNA ImmunoPrecipitation (fRIP-Seq), a sensitive method for cataloging RNA-protein interactions, to survey the RNA associated with a panel of 24 chromatin-associated and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detected enrichment for hundreds to thousands of both noncoding and mRNA transcripts. We found that the enriched sets of RNA share biochemical, functional, and epigenetic properties. Thus, these data provide strong evidence that non-random RNA association is a common feature across diverse classes of chromatin modifying complexes. RNA associated with 24 different proteins using fRIP was compared to total RNA-seq

2016-07-03 | E-GEOD-67963 | biostudies-arrayexpress

Tranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.

Project description:Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. We detected widespread interactions between RNA binding proteins (RBPs) and various families of TE-derived sequence in the CLIP-Seq data. Alignment coverage clustered on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific motifs for many RBPs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggest that TEs have appropriated existing sequence preferences of the RBP. Upon depletion of the RBPs, transcripts possessing TE-derived binding sites were similarly regulated as those bound in nonrepetitive sequence. However, in a few cases the effect of RBP binding depended on the specific TE family boundM-bM-^@M-^Te.g., the ubiquitously expressed RBP HuR conferred opposite effects on stability to transcripts when bound to Alu elements versus other families. Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. HuR formaldehyde RIP-Seq in K562 cells, with RIP and input sequenced in triplicate.

2014-09-10 | E-GEOD-61238 | biostudies-arrayexpress

Systematic Identification of Protein Phosphorylation-Mediated Interactions

Project description:Protein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites but the functions of a vast majority of these sites remain unknown, with less than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach for identifying the phosphorylation dependence of protein assemblies in a systematic manner. A combination of non-specific protein phosphatase treatment, size-exclusion chromatography, and mass spectrometry allowed us to identify changes in protein interactions after the removal of phosphates. With this approach we were able to identify 316 proteins involved in phosphorylation-sensitive interactions. We recovered known phosphorylation-dependent interactors such as the FACT complex and spliceosome, as well as identified novel interactions such as the tripeptidyl peptidase TPP2 and the supraspliceosome component ZRANB2. More generally, we find phosphorylation-dependent interactors to be strongly enriched for RNA-binding proteins, providing new insight into the role of phosphorylation in RNA binding. By searching directly for phosphorylated amino acid residues, we identified the likely regulatory phosphosites on ZRANB2 and FACT complex subunit SSRP1. This study provides both a method and resource for obtaining a better understanding of the role of phosphorylation in native macromolecular assemblies.

2020-09-22 | PXD021422 | Pride

Single-cell RNA sequencing of human embryonic stem cell-derived pancreatic cells enriched for early endocrine progenitors using a novel dual NEUROG3-reporter

Project description:Human embryonic stem cells with one allele of the NEUROG3 gene genetically modified into a fusion gene NEUROG3-LINKER-TAGRFPT-P2A-EGFP-NLS were differentiated into the pancreatic lineage until Stage 4 Day 1 of the in vitro differentiation protocol (Rezania et al., 2014, as modified in Petersen et al., 2017). The cells were index-sorted according to their GFP expression to enrich for low GFP and high GFP cells, and deep single-cell RNA-seq was performed using the plate-based Smart-seq2 platform (Picelli et al. 2014).

2022-12-31 | E-MTAB-11208 | biostudies-arrayexpress

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (ChIP-Seq yeast)

Project description:Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5meC levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo. Yeast ChIP sequencing

2015-04-02 | E-GEOD-66909 | biostudies-arrayexpress

Systematic discovery of endogenous ribonucleoprotein complexes - RNA DIF-FRAC mouse embryonic stem cell

Project description:The associated files are mass spec data from size exclusion chromatographic separations of mouse embryonic stem cells with and without RNAse A treatment.

2019-10-18 | PXD014607 | Pride

The Diagnostic Value of Salivary microRNA in Esophageal Cancer

Project description:Tissue microRNAs (miRNAs) can detect cancers and predict prognosis. Several recent studies reported that tissue, plasma, and saliva miRNAs share similar expression profiles. In this study, we investigated the diagnostic value of salivary miRNAs (including whole saliva and saliva supernatant) for detection of esophageal cancer. By Agilent microarray, six deregulated miRNAs from whole saliva samples from seven patients with esophageal cancer and three healthy controls were selected. The six selected miRNAs were subjected to validation of their expression levels by RT-qPCR using both whole saliva and saliva supernatant samples from an independent set of 39 patients with esophageal cancer and 19 healthy controls.

2012-10-03 | E-GEOD-41268 | 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