Browse
Submit Data
Databases
API
Help

Dataset Information

222 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CLIC4 interacting proteins - To identify proteins in human pulmonary artery endothelial cells that interact with CLIC4

ABSTRACT: To identify proteins in human pulmonary artery endothelial cells that interact with CLIC4

INSTRUMENT(S): LTQ

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Pulmonary Artery Endothelial Cell

DISEASE(S): Pulmonary Hypertension

SUBMITTER: Vahitha Abdul Salam

LAB HEAD: Vahitha Abdul Salam

PROVIDER: PXD008709 | Pride | 2018-10-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	130424_03.RAW	Raw
	130424_03.srf	Other
	130424_04.RAW	Raw
	130424_04.srf	Other
	130424_05.RAW	Raw

Items per page:

1 - 5 of 49

Similar Datasets

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

Project description:Here we delineate the roles of RNA binding for WDR5 function on chromatin state and murine embryonic stem cell (ESC) maintenance. Examination of global transcriptional changes and mapping genome-wide transcription factors occupancy at distinct time points during the transdifferentiation process

2014-02-12 | E-GEOD-53035 | biostudies-arrayexpress

Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [Affymetrix]

Project description:Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embyonic kidney cells and examined combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Among the targets ZFP36 binds and negatively regulates the mRNA of genes encoding proteins necessary for immune function and cancer, and other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance from ZFP36 overexpression independent of effects from confounding features, such as 3M-bM-^@M-^Y UTR length. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes. ZFP36 preferentially interacts with and regulates AU-rich sequences while ELAVL1 prefers predominantly U- and CU-rich sequences. RNA target specificity identified by global in vivo ZFP36-mRNA interactions were quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 both bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to untangle the in vivo combinatorial regulation by RNA-binding proteins. Five biological replicates for each of the four sample classes -> Parental and EGFP-ZFP36 HEK293 cells treated with either doxycycline or water.

2013-12-24 | E-GEOD-53183 | biostudies-arrayexpress

Mass spectrometry analysis of two RNA-binding proteins, RBP23 and DRBD2, partners of different Poly(A) Binding proteins (PABP) homologues in Leishmania infantum

Project description:RNA binding proteins (RBP) have multiple roles associated with mRNA stability and translation. In the Leishmania genus, three Poly(A) Binding Proteins (PABP) were encoded with yet undefined functional distinctions but previous studies of mass-spectrometry identified RBPs differentially associated with PABP1 and PABP2, including RBP23 and DRBD2, respectively. Further characterization of both RBPs were performed through co-immunoprecipitation of proteins with HA-tagged RBP23 and DRBD2 from Leishmania infantum cytoplasmic extract cells, combined to mass spectrometry analysis. The analysis confirmed a strong association between RBP23 and PABP1, as well as with the EIF4E4/EIF4G3, a typical translation initiation complex, while DRBD2 was found to be more associated with PABP2 and a large number of different protein partners. Our studies expand the knowledge about RBPs function and their partners during Leishmania mRNA translation/metabolism.

2021-11-02 | PXD022480 | Pride

ChIP-seq of Arabidopsis ARGONAUTE-small RNA interactions in Arabidopsis thaliana identified by high-throughput sequencing

Project description:The goal of this study was to identify small RNA-ARGONAUTE interactions in Arabidopsis. Co-immunoprecipitation assays followed by high-throughput sequencing were done to identify small RNA associated with HA-AGO2 and HA-AGO7. Experiment Overall Design: Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets. Experiment Overall Design: Note: Raw data files requested, however, the submitter declined to provide them.

2009-08-30 | E-GEOD-12037 | biostudies-arrayexpress

Genome-wide analysis of genes regulated by ARR22 overexpression.

Project description:The experiment was designed to enable comparison of Pro35S:ARR22:HA in the presence of DEX or absence of DEX.

2013-07-27 | E-MEXP-3685 | biostudies-arrayexpress

FOXO3a Is A Major Target Of Inactivation By PI3K/AKT Signaling In Aggressive Neuroblastoma

Project description:Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system with a highly variable prognosis. Activation of the PI3K/AKT pathway in neuroblastoma is correlated with poor patient prognosis, but the precise downstream effectors mediating this effect have not been determined. Here, we identify the forkhead transcription factor FOXO3a as a key target of the PI3K/AKT pathway in neuroblastoma. FOXO3a expression was elevated in low stage neuroblastoma tumors and normal embryonal neuroblasts, but reduced in late stage neuroblastoma. Inactivation of FOXO3a by AKT was essential for neuroblastoma cell survival. Treatment of neuroblastoma cells with the dual PI3K/mTOR inhibitor PI-103 activated FOXO3a and triggered apoptosis. This effect was rescued by FOXO3a silencing. Conversely, apoptosis induced by PI-103 or the AKT inhibitor MK-2206 was potentiated by FOXO3a overexpression. Further, levels of total or phosphorylated FOXO3a correlated closely with apoptotic sensitivity to MK-2206. In clinical specimens, there was an inverse relationship between gene expression signatures regulated by PI3K signaling and FOXO3a transcriptional activity. Moreover, high PI3K activity and low FOXO3a activity were each associated with an extremely poor prognosis. Our work indicates that expression of FOXO3a and its targets offer useful prognostic markers as well as biomarkers for PI3K/AKT inhibitor efficacy in neuroblastoma. Affymetrix U133 Plus 2.0 profiling of SY5Y-TetR-FOXO3A cells treated with doxycycline and/or the PI3K/mTOR inhibitor PI-103. Each condition profiled in triplicate.

2013-05-01 | E-GEOD-42762 | biostudies-arrayexpress

Proteomics of CLIC4 overexpressing human pulmonary artery endothelial cells

Project description:To identify CLIC4 effectors by studying proteins expressiosn altered by CLIC4 overexpression in human pulmonary artery endothelial cells.

2018-10-16 | PXD008714 | Pride

GPR35 promotes glycolysis, proliferation and oncogenic signalling by engaging with the sodium potassium pump

Project description:We used human embryonic kidney HEK293T cells transfected with human GPR35 cDNAs as baits that were engineered to express Strep or hemagglutinin (HA) tags at the C terminus to perform an unbiased proteomics survey for GPR35 interaction partners.

2019-11-12 | PXD011269 | Pride

Actively translating transcriptome (Ribotag) profiling of mouse retinal endothelial cells during postnatal development

Project description:Angiogenesis, a process mediating the expansion of vascular beds in many physiological and pathological settings, requires dynamic changes in endothelial cell (EC) behavior. The molecular mechanisms governing EC activity during different phases of vascular growth, remodeling, maturation, and quiescence remain elusive. Here, we have employed actively translating transcriptome analysis of mouse retinal ECs for the characterization of dynamic gene expression changes during postnatal development and the identification of critical angiogenic factors.

2020-08-28 | E-MTAB-5087 | biostudies-arrayexpress

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [RNA-Seq]

Project description:Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3M-bM-^@M-^YUTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors. To assess whether miRNAs are regulated by LIN28B we analyzed the miRNA levels of LIN28B overexpressing and LIN28B-depleted cells using small RNA cDNA library sequencing. The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells.

2013-02-26 | E-GEOD-44568 | 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