Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Label-Free Quantitative Proteomics Data for NPC Permeability Barrier Dynamics

ABSTRACT: This dataset contains label-free quantitative (LFQ) mass spectrometry analyses of proteins associated with affinity-purified isolated native Saccharomyces cerevisiae nuclear pore complexes (NPCs). The study compared wild type NPCs (+CP WT NPCs) with NPCs frozen at -80°C, or incubate in buffer at 4°C for the indicated days, which led to loss of the central plug (−CP WT NPCs). +CP WT NPCs were also compared to NPCs obtained from mutant strains where nearly half of the mass of FG repeats have been deleted (ΔFG), or increased by doubling the size of the FG region of Nsp1 (Nsp1FGx2). LFQ analyses indicated that the presence of the central plug is strongly associated with a persistent fraction of karyopherins (Kaps) and other factors residing within the NPC. In contrast, the quantities of other NPC components remained stable within the precision of the method for WT and mutant NPCs.

INSTRUMENT(S):

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

SUBMITTER: Wenzhu Zhang

LAB HEAD: Brian T. Chait

PROVIDER: PXD069104 | Pride | 2025-10-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230201_Trevor-NPC-Nsp1DoubleFG-10ppm_ProteinGroupReport.xls	Xls
	20250929_Javi-NPC-timers-day0-day5_ProteinGroupReport.xls	Xls
	Javi-FG-Del-20210216_ProteinGroupReport.xls	Xls
	Raw-NPC-FG-Del.zip	Other
	Raw-NPC-timecrs-day0-day5.zip	Other

Items per page:

1 - 5 of 8

Similar Datasets

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore

Project description:Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the g-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs.

2018-05-22 | PXD008334 | Pride

Proteomic analysis of WT and AP-2 KO NPCs at DIV3

Project description:Full proteome analysis of WT and AP-2 KO NPCs at DIV3 to detect dysregulated proteins.

2023-12-11 | PXD047200 | Pride

SMRT compounds abrogate cellular phenotypes of Ataxia Telangiectasia in neural derivatives of patient specific hiPSCs

Project description:gene expression profiling of WT fibroblasts, hiPSCs, and NPCs compared to the same cell types isolated from patients with Ataxia Telangiectasia gene expression profiling was carried out with Affymetrix Hg133 2.0 plus chips fibroblasts, hiPSCs, hESCs, and NPCs were isolated and compared by gene expression

2013-04-01 | E-GEOD-45030 | biostudies-arrayexpress

Microarray analysis of Nurr1 and Foxa2 synergisitic effect for DA neuron induction

Project description:Analysis of dopaminergic neuronal gene expression changes by Nurr1 and/or Foxa2 overexpression. Result provides that Foxa2 potentiates Nurr1-induced DA neuronal phenotype gene expression. To identify the syergism of Nurr1 and Foxa2 for developing DA neural precursors, neural precusor cells (NPCs) isolated from embryonic brain were treated control, Nurr1, Foxa2 and Nurr1-Foxa2 retrovirus. After treatment of retroviruses, NPCs were cultrued in N2 media withdrawn mitogen (bFGF, EGF) for differetiation of DA neuron. Total RNA was obtained from NPCs in differentiation day 2.

2014-01-16 | E-GEOD-54086 | biostudies-arrayexpress

Expression profiles in HMGN1-overexpressed neural precursor cells

Project description:Neural precursor cells (NPCs) are multipotent cells that can generate neurons, astrocytes, and oligodendrocytes in the mammalian central nervous system. Although high mobility group nucleosomal binding domain 1 (HMGN1) was highly expressed in NPCs, its functions in neural development are not fully understood. We performed microarray analysis to examine changes in gene expression between control and HMGN1-overexpressed NPCs. NPCs derived from E11.5 mouse forebrains were infected with control or HMGN1 retrovirus in the presence of fibroblast growth factor 2 (FGF2) and epidermal growth factor (EGF). Three days after infection, the virus-infected NPCs were dissociated and seeded on poly-D-lysine -coated dishes, and subsequently the cells were cultured for 1 day without FGF2 and EGF.

2014-09-01 | E-GEOD-57534 | biostudies-arrayexpress

BET Bromodomain inhibition promotes neurogenesis while inhibiting gliogenesis in neural progenitor cells

Project description:Neural stem cells (NSCs) and progenitor cells (NPCs) are increasingly appreciated to hold great promise for regenerative medicine to treat CNS injuries and neurodegenerative diseases. However, evidence for effective stimulation of neuronal production from endogenous or transplanted NPCs for cell replacement with small molecules remains limited. To identify novel chemical entities/targets for neurogenesis, we had established a NPC phenotypic screen assay and validated it using known small-molecule neurogenesis inducers. Through screening small molecule libraries with annotated targets, we identified BET bromodomain inhibition as a novel mechanism for enhancing neurogenesis. BET bromodomain proteins, Brd2, Brd3, and Brd4 were found to be downregulated in NPCs upon differentiation, while their levels remain unaltered in proliferating NPCs. Consistent with the pharmacological study using bromodomain selective inhibitor (+)-JQ-1, knockdown of each BET protein resulted in an increase in the number of neurons with simultaneous reduction in both astrocytes and oligodendrocytes. Gene expression profiling analysis demonstrated that BET bromodomain inhibition induced a broad but specific transcription program enhancing directed differentiation of NPCs into neurons while suppressing cell cycle progression and gliogenesis. Together, these results highlight a crucial role of BET proteins as promising epigenetic regulators in NPC development and suggest a therapeutic potential of BET inhibitors in treating CNS injury and neurodegenerative diseases. NPCs were treated with (+)-JQ-1 or inactive enantiomer (-)-JQ-1 at 0.2 Î¼M or 0.5 Î¼M for 12 and 24 hrs in differentiation medium. The experiments were carried out in 3 independent preparations of NPCs (triplicates)

2016-07-24 | E-GEOD-77988 | biostudies-arrayexpress

Extracellular vesicles from neural stem cells transfer IFN-? via Ifngr1 to activate Stat1 signalling in target cells

Project description:The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-?) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-? bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-?/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-?/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system. polyA RNA profiling of Neural Stem/Progenitor cells (NPCs) cultured in basal/Th1/Th2 conditions, of Exosomes derived from NPCs cultured in basal/Th1/Th2 conditions and of EVs derived from NPCs cultured in Basal/Th1/Th2 conditions. Total RNA was purified using Trizol. Purity and integrity were confirmed by BioAnalyser (Agilent). Paired End library construction and poly-A selection were performed by EASIH (The Eastern Sequence and Informatics Hub, University of Cambridge, Cambridge) according to the Illumina standard protocol. Sequencing was performed by EASIH using Illumina GAII.

2014-09-22 | E-GEOD-33527 | biostudies-arrayexpress

Transcription profiling of mouse ES cells, neural precursor cells and embryonic fibroblasts

Project description:Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5. Experiment Overall Design: 3 replicates of wt ES cells, 3 replicates of wt NPCs obtained by in vitro differentiation, 2 replicated of primary MEFs

2008-06-15 | E-GEOD-8024 | biostudies-arrayexpress

Delayed cell cycling in DS Ts1Cje neural precursor cells results in gene expression dysregulation

Project description:Down syndrome neurophenotypes are characterized by mental retardation and a decreased brain volume. In order to identify whether deficits in proliferation, differentiation or survival could be responsible for this phenotype, neural precursor cells (NPCs) were isolated from the developing E14 neocortex of Down syndrome partial trisomy Ts1Cje mice and euploid (WT) littermates. Proliferation, cell differentiation and cell death assays revealed that Ts1Cje NPCs proliferated at a slower rate, due to a longer cell cycle and that a greater number of cells were positive for glial fibrillary acidic protein. An increase in Ts1Cje NPC cell death was also noted. Gene expression profiling was conducted on RNA extracted from Ts1Cje and WT NPCs. Approximately 54% of triploid gene expression ratios were significantly greater than the expected diploid gene ratio of 1.0. A number of diploid genes associated with differentiation, glial function and proliferation were dysregulated. The evidence points to a delay in cellular cycling that could exert stress on the NPC population, which might result in cellular death and a mobilization of glial cell survival responses. Importantly, these phenotypic changes, which mimic those seen in Down syndrome individuals, do not require over-expression of amyloid precursor protein (App) or soluble superoxide dismutase 1 (Sod1). In conclusion, early developmental proliferation deficits in Down syndrome result in secondary morphological changes that can impact on cognitive development and function. Keywords: Down syndrome, Neocortical precursor cells, transcriptome, proliferation Neural precursor cells (NPCs) were isolated from mouse E14 neocortex of Down syndrome Ts1Cje mice and euploid littermates. We compared gene expression profiles from trisomic and wild-type cells using pangenomic microarrays.

2010-05-19 | E-GEOD-9805 | biostudies-arrayexpress

L1-associated genomic regions are deleted in somatic cells of the healthy human brain â RNA-Sequencing

Project description:RNA-Seq of NPCs with knowckdowns for PWRN2 and controls

2016-08-28 | E-MTAB-4830 | biostudies-arrayexpress