Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome for Usp11 knockout E17.5 cortex

ABSTRACT: Since Usp11 encodes a DUB, we reasoned that Usp11 deficiency may lead to increased ubiquitination and destabilization of a protein that functions in neuronal differentiation and migration.To define the molecular mechanism of Usp11 deficiency on cortical development, we performed a label-free quantitative liquid chromatography-tandem Mass Spectrometry (LC-MS/MS) analysis to detect the protein expression profiles in E17.5 WT and Usp11 KO cortices in four biological repeats.

INSTRUMENT(S): LTQ Orbitrap, Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Generation Of Neurons

SUBMITTER: Shang Yin Chiang

LAB HEAD: Shang Yin, Chiang

PROVIDER: PXD021587 | Pride | 2021-01-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Cardiac Myofibrillogenesis is Spatiotemporally Modulated by the Molecular Chaperone UNC45B

Project description:Sarcomeres are fundamental to cardiac muscle contraction. Their impairment can elicit cardiomyopathies, leading causes of death worldwide. However, the molecular mechanism underlying sarcomere assembly remains obscure. We used human embryonic stem cell (hESC)-derived cardiomyocytes (CMs) to reveal step-wise spatiotemporal regulation of core cardiac myofibrillogenesis-associated proteins.

2023-10-24 | PXD042075 | Pride

A proteomic approach for systematic mapping of human deubiquitinating enzymes substrates

Project description:In the present study we implemented the bioUb approach to identify DUB substrates in a systemic manner. DUBs have been individually silenced so that the ubiquitination levels of their respective substrates are increased, and hence, upon isolation, susbtrates have been detected by mass spectrometry. Here we report quantitative proteomic data of the putative substrates of 5 human DUBs: USP1, USP7, USP9X, USP11 and USP42.

2021-04-29 | PXD025443 | Pride

RNA-seq of KYSE410 cells expressing control, USP11 or ARID1A-targeting shRNAs

Project description:We examined gene expression level in KYSE410 cells expressing control, USP11 or ARID1A-targeting shRNAs to study the mechanism underlying the tumor suppressive effect of ARID1A and USP11.

2019-11-30 | GSE132359 | GEO

USP11/LSH/CYP24A1 axis activation underlies calcium homeostasis and potentiates the resistance of colorectal cancer cells to ferroptosis

Project description:To explore the key downstream factors for USP11 stable LSH regulation, we performed transcriptome analysis using controls, USP11 knockdown, and LSH knockdown HCT116 cells We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

2023-07-12 | GSE211866 | GEO

RNA sequencing results of wild type and knockout USP11 in E13.5 or E18.5 of cortex based on IlluminaNovaSeq 6000 platform

Project description:We found that USP11 expression perturbed neurogenesis.

2023-01-01 | GSE143976 | GEO

Single-cell transcriptome analysis of Myt1l mutant mouse cortices at birth.

Project description:We examined the effect of Myt1l deficiency in the cortices of mice at birth on the single cell level. Homozygous Myt1l deficiency resulted in postnatal lethality, and mutant mice presented increased expression of non-neuronal genes in neurons.

2023-02-14 | GSE171326 | GEO

Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival

Project description:Background: Autophagy plays important roles in cell homeostasis and protein quality control. Long non-coding RNAs (lncRNAs) have been revealed as an emerging class of autophagy regulators, but the majority of them function in regulating the expression of autophagy-related genes. LncRNAs that directly act on the core autophagic proteins remain to be explored. Methods: Immunofluorescence staining and Western blotting were used to evaluate the function of BCRP3 in autophagy and aggrephagy. RNA pull down and RNA immunoprecipitation were used to evaluate the interaction of BCRP3 with its target proteins. Phosphatidylinositol 3-phosphate ELISA assay was used to quantify the enzymatic activity of VPS34 complex. qRT-PCR analysis was used to determine BCRP3 expression under stresses, whereas Mass spectrometry and Gene Ontology analyses were employed to evaluate the effect of BCRP3 deficiency on proteome changes. Results: We identify lncRNA BCRP3 as a positive regulator of autophagy. BCRP3 is mainly localized in the cytoplasm and binds VPS34 complex to increase its enzymatic activity. In response to proteotoxicity induced by proteasome inhibition or oxidative stress, BCRP3 is upregulated to promote aggrephagy for the clearance of ubiquitinated protein aggregates. Proteomics analysis revealed that BCRP3 deficiency under proteotoxicity results in a preferential accumulation of proteins acting in growth inhibition, cell death, apoptosis, and Smad signaling. Accordingly, BCRP3 deficiency in proteotoxic cells compromises cell proliferation and survival, which is mediated in part through the upregulation of TGF-/Smad2 pathway. Conclusions: Our study identifies BCRP3 as an RNA activator of the VPS34 complex and a key role of BCRP3-mediated aggrephagy in protein quality control and selective degradation of growth and survival inhibitors to maintain cell fitness.

2022-05-20 | PXD030756 | Pride

Bulk transcriptome analysis of Myt1l mutant mouse cortices across development.

Project description:We examined the effect of Myt1l deficiency in the cortices of mice during developement. Homozygous Myt1l deficiency resulted in postnatal lethality, and mutant mice presented gene expression changes associated with developmental delays and resembled changes observed in autism spectrum disorder patients.

2023-02-14 | GSE171325 | GEO

Identification of transcriptional changes upon genetic deletion of Vhl, Pbrm1 and double deletion of both Vhl and Pbrm1

Project description:To determine why double deficiency of Vhl and Pbrm1 but not single deficiency of either gene resulted in ccRCC, we performed gene expression profiling of RNA isolated from renal cortices of 3-month-old WT, VhlF/FKsp-Cre, Pbrm1F/FKsp-Cre, and VhlF/FPbrm1F/FKsp-Cre mice.

2017-03-06 | GSE83597 | GEO

Versatile regulation of autophagy by the deubiquitinase USP11

Project description:Ubiquitination is a versatile post-translational modification known to regulate autophagy. Here, we show that loss of the deubiquitinase USP11 leads to an increase in the autophagic flux. To investigate the molecular details of how USP11 impacts autophagy, we determined interaction partners of USP11 using an affinity purification-mass spectrometry approach. GFP-tagged, catalytically inactive USP11(C318S) was overexpressed in 293 cells. After 4 hour treatment with Torin 1, an inhibitor of mTOR that induces autophagy, cells were lysed and samples further processed for analysis. Catalytically inactive USP11 was used to increase the chances of capturing both interaction partners and potential substrates. We identified many autophagy-related proteins that co-precipitated with USP11, suggesting that USP11 does not regulate autophagy via a single substrate, but that the observed phenotype is the sum of many interactions, each of which should be independently investigated in more detail. Our work focused on elucidating the regulation of autophagy via the lipid kinase complex PI3KC3 complex I, as one of its components (VPS15) was identified in our USP11 interactome data. PI3KC3 complex I is crucial for initiation of autophagosome formation at the endoplasmatic reticulum. USP11 knockout caused an increase in complex activity, which could explain enhanced autophagy in these cells.

2022-02-16 | PXD022143 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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