Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of gene expression regulated by nucleolin in mouse embryonic stem cells

ABSTRACT: To further explore the function and underlying mechanism of nucleolin in embryonic stem cells (ESCs), we compared the transcription profile of tetracycline (Tc)-inducible EGFP (as a control) or nucleolin siRNA expression-stable ESCs cultured with or without Tc for 3 days, and identified distinct classes of up- and down-regulated genes by nucleolin in mouse ESCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE23993 | GEO | 2011/10/20

SECONDARY ACCESSION(S): PRJNA130283

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide analysis of gene expression regulated by nucleolin in mouse embryonic stem cells

Project description:To further explore the function and underlying mechanism of nucleolin in embryonic stem cells (ESCs), we compared the transcription profile of tetracycline (Tc)-inducible EGFP (as a control) or nucleolin siRNA expression-stable ESCs cultured with or without Tc for 3 days, and identified distinct classes of up- and down-regulated genes by nucleolin in mouse ESCs. Total RNA obtained from CGR8 ES cells stably integrated with Tc-inducible siRNA EGFP, nucleoin-1 or nucleolin-2 cultured with or without Tc for 3 days, and then hybridized to Illumina Sentrix Mouse-6 v2.0 BeadChips. Three replicates each condition.

2011-10-19 | E-GEOD-23993 | biostudies-arrayexpress

Identification of nucleolin-targeted RNA transcripts

Project description:Although Rrp6 contains a helicase and RNase D domain at the C-terminus, it is not involved in stable RNA interactions. We thus hypothesized that mRrp6-mediated nucleolar inflammatory RNA degradation may depend on the pre-mRNA substrate that is delivered to the mRrp6-exosome complex by nucleolin as a guide factor. To demonstrate this possibility, we examined nucleoplasmic RNAs which were bound to nucleolin through RNA-IP-sequencing at the late time points of LPS stimulation.

2021-02-28 | GSE95528 | GEO

Analysis of Nucleolin depletion impact on the KRAS-induced proteomic changes in mouse Pancreatic ductal adenocarcinoma cells.

Project description:To reveal the role of Nuclelin (Ncl) downstream of mutant KRAS in shaping the proteome of Pancreatic Ductal Adenocarcinoma (PDAC) cells, we carried out a quantitative proteomics analysis of tumour cells isolated from an inducible mouse model of PDAC (iKras PDAC) (Ying et al., 2012). In this model, oncogenic Kras (G12D) expression can be controlled by administration of doxycycline (Dox). Tandem Mass Tagging (TMT) was employed for quantitative analysis of Dox induced (24hrs) vs. non-induced iKras-PDAC cells, from control or Nucleolin depleted settings. Two independent siRNA oligos were used against Ncl. All samples barcoded and pooled together using TMT 6plex labelling kit (Thermo).

2023-02-12 | PXD038338 | Pride

A Novel Role for Nucleolin in Splice Site Selection

Project description:In search for nuclear partners of initiator-tRNA, previously shown to be involved in a quality control of splice site selection, we identified nucleolin (NCL) as specifically and directly bound to it in the nucleus and not in the cytoplasm (using affinity purification of UV crosslinked nuclear initiator-tRNA followed by mass spectrometry). To further explore the role of NCL in splice site selection, we knocked down NCL. We report the activation of 399 latent splice sites upon NCL knockdown, as revealed by RNA deep sequencing of siRNA treated NCL compared to control siRNA. Our study identifies NCL as the first protein component of this quality control mechanism of splice site selection. Our study thus establishes an experimental strategy and computational pipeline that could be used to identify other components of this quality control mechanism.

2022-03-08 | GSE142836 | GEO

Gene expression of nucleolin or TRA2B4-silencing HCT116 cells

Project description:TRA2β4 is transcribed from the human transformer 2β(TRA2B) gene and overexpressed in colon cancer cells. Nucleolin is one of RNA-binding proteins to regulate cell survival and proliferation. In this study, TRA2β4 and Nucleolin levels were reduced in colon cancer HCT116 cells and gene expression levels were measured using microarray analysis.

2018-04-06 | GSE112758 | GEO

Analysis of RNA localization in nucleolin deficient axons

Project description:We previously showed that the RNA binding protein Nucleolin is localized to axons of DRG sensory neurons by interaction with the molecular motor Kinesin-1 (Kif5A) and subsequently localizes importin beta1 mRNA there (Perry et al., 2016). In this work, we created a mouse with a heterozygous deletion of the domain in nucleolin responsible for the Kif5A interaction and showed that nucelolin protein levels are reduced in the axons of dorsal root ganglia neurons in this mouse model. The goal of this study was to identify RNAs who's axonal localization is affected by this perturbation.

2021-07-23 | GSE142096 | GEO

Binding of Nucleolin to HBV cccDNA

Project description:Binding of Nucleolin to HBV cccDNA

| PRJNA509631 | ENA

Nucleolin is a cell surface receptor of C1QTNF4

Project description:C1QTNF4 is a secreted protein that is structurally unique within the C1QTNF family, a family of proteins that have structural homology with both complement C1q and the tumor necrosis factor superfamily. The role of C1QTNF4 in immunity and inflammation remains poorly defined and a cell surface receptor has yet to be identified. Here we performed co-immunoprecipitation with subsequent mass spectrometric analysis in order to identify a cell surface receptor of C1QTNF4. We report identification of nucleolin as a cell surface binding partner of C1QTNF4. Nucleolin may serve as a docking molecule for C1QTNF4 and act in a context-dependent manner through co-receptors. Having identified nucleolin as a cell surface receptor is a further step to understanding C1QTNF4’s function in the healthy immune system.

2021-03-21 | PXD023088 | Pride

Integrated analysis identifies key determinants of embryonic stem cell identity and homeostasis

Project description:Despite RNAi-based screens to uncover genes controlling embryonic stem cell (ESC) identity, the pluripotency network remains poorly characterized, as does the precise molecular mechanisms underlying the balance between self-renewal and differentiation. Here we carried out a systematic meta-analysis of published gene expression data to rank-order genes based on their likelihood of regulating ESC identity. Not only did our analysis correctly rank known pluripotency-associated genes atop the list, but it also helped unearth many novel determinants of ESC identity including several components of functionally distinct complexes, as determined using RNAi. We focus on our top-hit Nucleolin, and characterize its mechanistic role in the maintenance of ESC homeostasis by shielding from differentiation-inducing redox imbalance-induced oxidative stress. Notably, we identify a conceptually novel mechanism involving a Nucleolin-dependent bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our gene ranks represent a rich and valuable resource for uncovering novel ESC regulators. Microarray gene expression profiling in E14Tg2a mESCs after transfection with indicated siRNAs: Ncl siRNA #1 (Invitrogen, 17975-MSS206961) Ncl siRNA #2 (Invitrogen, 17975-MSS275939), and Control siRNA duplex targeting firefly luciferase.

2014-03-26 | E-GEOD-47872 | biostudies-arrayexpress

AP-MS interactome studies on mutant GATAD1 variants

Project description:Tetracycline inducible, stable HEK-293 cell lines expressing BirA-FLAG-GATAD1 variants were generated using the Flp-In system. Besides WT GATAD1, S102P (ProMut), S102D (AspMut), and S102A (AlaMut)mutant variants were studied. The goal of the experiment was to compare the differences in the interactomes of WT GATAD1 and its mutant counterparts. As a control samples not induced with tetracycline were used.

2024-02-15 | PXD046950 | Pride

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