Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

UAG suppression in HEK293T cells

ABSTRACT: HEK293T cells, stably transfected with pyrrolysine UAG suppressor tRNA and aminoacyl tRNA synthetase, for the co-translational incorporation of Boc-protected lysine.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Eyal Arbely

LAB HEAD: Eyal Arbely

PROVIDER: PXD016728 | Pride | 2020-02-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HF1_9641_EAR_boc-nt2.raw	Raw
	HF1_9641_EAR_boc-nt3_190619204817.raw	Raw
	HF1_9641_EAR_boc-nt4.raw	Raw
	HF1_9641_EAR_boc-nt5_190620025225.raw	Raw
	HF1_9641_EAR_boc1.raw	Raw

Items per page:

1 - 5 of 9

Publications

Translational read-through promotes aggregation and shapes stop codon identity.

Kramarski Lior L Arbely Eyal E

Nucleic acids research 20200401 7

Faithful translation of genetic information depends on the ability of the translational machinery to decode stop codons as termination signals. Although termination of protein synthesis is highly efficient, errors in decoding of stop codons may lead to the synthesis of C-terminally extended proteins. It was found that in eukaryotes such elongated proteins do not accumulate in cells. However, the mechanism for sequestration of C-terminally extended proteins is still unknown. Here we show that 3'- ...[more]

PMID: 32128584

Similar Datasets

Mass spectrometry identification of proteins of isolated auditory and vestibular hair cells using data-independent and data-dependent acquisition

Project description:Hair cells undergo postnatal development that leads to formation of their sensory organelles, synaptic machinery, and in the case of cochlear outer hair cells, their electromotile mechanism. To examine the proteome changes over development, we isolated pools of 5000 Pou4f3-Gfp positive or negative cells from the cochlea or utricles; these cell pools were analyzed by data-dependent and data-independent acquisition (DDA and DIA) mass spectrometry. DDA data were used to generate spectral libraries, which enabled identification and accurate quantitation of specific proteins using the DIA datasets. We also isolated and pooled individual inner and outer hair cells from adult cochlea and compared their proteomes to those of developing hair cells. The DDA and DIA datasets will be valuable for accurately quantifying proteins in hair cells and non-hair cells over this developmental window.

2017-09-18 | PXD006240 | Pride

Global proteome of Atg5flox:CamKIIα-Cre:tdTomato FACS sorted WT and KO neurons

Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain excitatory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:CamKIIα-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:CamKIIα-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and excitatory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

2022-11-15 | PXD031552 | Pride

Proteomic profile of Campylobacter jejuni 11168 during in vitro growth in the presence or absence of penicillin

Project description:The proteomic makeup of three biological replicates of cells incubated for 24 h in MHB (control) or three biological replicates of cells incubated for 24 h in MHB containing 100 x MIC of penicillin G was analysed. The control or penicillin-treated cultures were stained with RSG and sorted using FACS into cells that did not fluoresce, cells that fluoresced weakly (dim) or cells that fluoresced brightly. Here we present the raw mass spectrometric data of control dimly stained cells and penicillin-treated brightly stained cells.

2020-10-20 | PXD021418 | Pride

Expression data from control, aged and activated neutrophils in mouse blood

Project description:Neutrophils provide immune protection against pathogens but also may promote tissue injury in inflammatory diseases. Although neutrophils are generally considered as a relatively homogeneous population, evidence for heterogeneity is emerging. Under steady-state conditions, neutrophil heterogeneity may arise from ageing and the replenishment by newly released neutrophils from the bone marrow. We used microarray to globally analyze gene expression in aged neutrophils and characterize the inflammatory programs that are activated during the aging process in the circulation. Control, aged and activated neutrophils were sorted directly from mouse blood for RNA extraction and hybridization on Affymetrix microarrays. We transfused whole blood and harvested donor neutrophils marked by the CD45.1 allele 6h later to derive neutrophils that had truly aged in vivo. Sorted neutrophils were compared to control donor neutrophils that had been transferred for only 10 min. Additionally, we harvested circulating neutrophils from TNF-? treated mice for comparison with neutrophils activated by systemic inflammation.

2015-09-24 | E-GEOD-69886 | biostudies-arrayexpress

Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment

Project description:Neutrophils rapidly respond to inflammation and infection, but to which degree their functional trajectories after mobilization from the bone marrow can be shaped within the circulation remains vague. Phenotypic changes of circulating neutrophils caused by systemic inflammation are thought to result from several factors, including a “left shift” of the neutrophil compartment towards younger bone marrow-derived subsets. However, experimental limitations have so far hampered neutrophil research in human disease. Here, using innovative fixation and single-cell-based toolsets, we profile the human and murine neutrophil transcriptome and proteome during steady state and bacterial infection. We find that peripheral priming of circulating neutrophils leads to plastic shifts dominated by conserved upregulation of antimicrobial genes across neutrophil substates, facilitating pathogen containment. We show the TLR4/NF-κB-signaling dependent upregulation of canonical neutrophil activation markers like CD177/NB-1 during acute inflammation, resulting in functional shifts in vivo. Importantly, blocking de novo RNA synthesis in circulating neutrophils abrogates these plastic shifts and prevents the adaptation of antibacterial neutrophil programs by upregulation of distinct effector molecules upon infection. In summary, these data underline transcriptional plasticity as a relevant mechanism of functional neutrophil reprogramming during acute infection to foster bacterial containment within the circulation. This adds to the understanding of competing modes of adaptation to inflammatory challenges by the neutrophil compartment.

2024-05-21 | PXD048335 | Pride

Engineered tRNAs suppress nonsense mutations in cells and in vivo

Project description:we introduce a strategy to repurpose sense-codon decoding tRNA into efficient suppressors of the three nonsense mutation-induced PTCs (UGA, UAG and UAA). The suppressor tRNAs restore function of a model and disease-related protein

2023-04-04 | GSE191048 | GEO

Cell-specific proteome analyses of human bone marrow upon aging.

Project description:Diminishing potential to replace damaged tissues is a hallmark for aging of somatic stem cells, but the mechanisms leading to aging remain elusive. We performed a proteome-wide analysis of human hematopoietic stem and progenitor cells (CD34+) along with five other cell types that constitute the bone marrow niche, namely, lymphocytes and precursors; monocytes/macrophages and precursors; granulocytic precursors and erythroid precursors, as well as mesenchymal stem/stromal cells. In total, we analyzed 270 samples from 59 human subjects. The data represents a valuable resource for further in-depth mechanistic analyses, and for validation of knowledge gained from animal models.

2018-07-20 | PXD007048 | Pride

Deconstruction of the GalNAc-Type O-Glycosylation Capacity of Human HEK293 Cells

Project description:Most proteins trafficking the secretory pathway of metazoan cells will acquire GalNAc-type O-glycosylation. GalNAc-type O-glycosylation is differentially regulated in cells by the expression of a repertoire of up to twenty genes encoding polypeptide GalNAc-transferase isoforms (GalNAc-Ts) that initiate O-glycosylation by catalyzing the attachment of GalNAc residues to select Ser and Thr residues. These GalNAc-Ts orchestrate the positions and patterns of O-glycans on proteins in poorly understood coordinated ways guided partly by the kinetic properties and substrate specificities of their catalytic domains and modulatory effects of their unique GalNAc-binding lectin domains. Here, we provide the hereto most comprehensive characterization of the non-redundant contributions of individual GalNAc-T isoforms to the O-glycoproteome of the human HEK293 cell line using quantitative differential O-glycoproteomics on a panel of isogenic HEK293 cell lines with knockout of GalNAc-T genes (GALNT1, T2, T3, T7, T10, or T11). We confirm that a major part of the O-glycoproteome is covered by redundancy, while distinct subsets of O-glycosites are covered by non-redundant GalNAc-T isoform-specific functions. We demonstrate that GalNAc-T7 and T10 as predicted from in vitro studies function in completion of high density O-glycosylated regions, while GalNAc-T11 selectively controls the site-specific O-glycosylation of low-density lipoprotein-related receptors in the linker regions between the ligand-binding LDLR class A repeats.

2019-06-24 | PXD009955 | Pride

AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice (mRNA-seq)

Project description:In this study, we utilized a mouse model of mucopolysaccharidosis type I (MPS-I) carrying a homozygous nonsense mutation in the Idua gene (Idua-W401X, TGG→TAG) to develop rAAV-delivered sup-tRNA therapeutics that can overcome a pathogenic UAG premature termination codon (PTC).

2021-11-30 | GSE189146 | GEO