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Secretome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3

ABSTRACT: Secretome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3 and control condition was assessed.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Alzbeta Chabronova

LAB HEAD: Mandy Peffers

PROVIDER: PXD046109 | Pride | 2024-05-22

REPOSITORIES: Pride

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			Action	DRS
	SC1.mgf	Mgf
	SC1.mzid.gz	Mzid
	SC1.raw	Raw
	SC2.mgf	Mgf
	SC2.mzid.gz	Mzid

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1 - 5 of 24

Publications

TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes.

van den Akker Guus G H GGH Chabronova Alzbeta A Housmans Bas A C BAC van der Vloet Laura L Surtel Don A M DAM Cremers Andy A Marchand Virginie V Motorin Yuri Y Caron Marjolein M J MMJ Peffers Mandy J MJ Welting Tim J M TJM

International journal of molecular sciences 20240505 9

Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribos ...[more]

PMID: 38732249

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Cellular proteome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3

Project description:Cellular proteome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3 and control condition was assessed.

2024-05-22 | PXD046111 | Pride

Ribosomal proteome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3

Project description:Ribosomal proteome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3 and control condition was assessed.

2024-05-22 | PXD046114 | Pride

ChIP-seq of Drosophila melanogaster plasmatocytes against various histone modifications

Project description:To identify the presence of different chromatin states in homogeneous primary cells, Drosophila melanogaster plasmatocytes were isolated from 3rd instar larvae and subjected to cross-linked ChIP-seq using antibodies against a range of H3 histone modifications and PolII.

2022-05-31 | E-MTAB-10707 | biostudies-arrayexpress

Time course experiment of 17Î²-estradiol (E2) treatment in the zebrafish

Project description:Transcriptional profiling of zebrafish (Danio rerio) livers comparing control untreated fish with fish treated with estrogen [17Î²-estradiol (E2)] for different time points (4, 12, 24, 48 hours). For the assay experimental design, RNA from one of three different E2-treated fish (representing three biological replicates) of each time point was hybridized with RNA that was pooled from liver samples of 15 untreated fish (control pool) on one chip.

2013-06-28 | E-GEOD-45562 | biostudies-arrayexpress

ChIP-seq of Drosophila melanogaster OregonR plasmatocytes at 6h post septic injury

Project description:Drosophila 3rd instar larvae were subjected to septic injury. After 6h plasmatocytes were isolated, fixed and subjected to ChIP-seq.

2022-05-31 | E-MTAB-10760 | biostudies-arrayexpress

Shotgun proteomics on sterile culture supernatant from S. aureus clinical isolates

Project description:Shotgun proteomics on sterile culture supernatant from S. aureus clinical isolates to determine proteins associated with pro-inflammatory phenotype.

2022-02-22 | PXD028604 | Pride

RNA-seq of Drosophila plasmatocyte mosaics which lack PRC2/H3K27me3

Project description:Genetic mosaics were induced in 3rd instar larvae by heatshock to generate H3K27R mutants, Su(z)12 mutants or E(z) mutants

2022-05-31 | E-MTAB-10762 | biostudies-arrayexpress

Whole proteome and Secretome analysis of Staphylococcus aureus ClpXP mutant strains

Project description:Staphylococcus aureus represents an opportunistic pathogen which utilizes elaborate quorum sensing mechanisms to precisely control the expression and secretion of virulence factors. Previous studies indicated a role of the ClpXP proteolytic system in controlling pathogenesis. While detailed transcriptome data for ClpP and ClpX is available, corresponding studies on the proteome, secretome and metabolome level are largely lacking. In order to decipher the functional roles of ClpP and ClpX more globally we utilized S. aureus deletion mutants of the corresponding genes for in-depth proteomic LC-MS/MS analysis. These studies were complemented by a ClpP active site mutant strain to monitor changes solely depending on the presence and not the activity of the protein. A comparison of these strains with wild type revealed e.g. downregulation of virulence, purine/pyrimidine biosynthesis, iron uptake and stress response. Correspondingly, a reduction of a subset of purine and pyrimidine metabolite levels independently confirmed these results. Interestingly, comparison between the ClpP knockout and ClpP active site mutant strains revealed characteristic differences in UMP biosynthesis and the staphyloferrin B pathway, suggesting that the presence of the protein, although inactive, is important for maintaining these processes. These results are not only of fundamental importance to understand the cellular role of ClpXP but also have implications for the development of novel virulence inhibitor classes.

2021-03-12 | PXD018932 | Pride

Single-cell transcriptional profiling of young-adult and aging (middle-aged) mouse anterior pituitary in steady-state conditions and after transgenically inflicted local damage

Project description:Adult pituitary stem cells (SC) are mainly dormant, yet in the case of damage the resident SC compartment shows swift activation. More in particular, following diphtheria toxin (DT)-triggered endocrine cell-ablation injury in the GHCre/iDTR mouse model (expressing the Cre recombinase under control of the Gh promoter, as well as the Cre-inducible DT receptor (iDTR)), the pituitary stem cell population is promptly activated displaying enhanced proliferative activity and expansion. Substantial regeneration of the depleted somatotropes is eventually observed after 5 to 6 months. However, this regenerative competence rapidly drops with age, and is no longer observed when mice get older (from 8-10 months of age). Virtually nothing is known about the molecular machinery driving the quiescent pituitary stem cells into activation (as observed following local injury), neither about how this route may change at advancing age. Here, we started to tackle this query by interrogating young (9-11 weeks) and old (14 months), damaged and undamaged pituitary (specifically, its major endocrine AP lobe) using single-cell RNA sequencing. We focused on the prompt stem cell reaction that occurs immediately upon the DT-induced local damage in the GHCre/iDTR model.

2021-06-15 | E-MTAB-10021 | biostudies-arrayexpress

Time-resolved proteomic profiling for CHO-K1 fed-batch cultivations

Project description:The majority of recombinant protein therapeutics are produced with Chinese Hamster Ovary (CHO) cells. Productivity depends on the initial cell line engineering in terms of integration site or choice of an appropriate promotor for the recombinant gene expression, as well as media and process parameter optimization. Here, proteomic profiling is used to identify optimization targets for a pharmaceutical relevant cell line system. Triplicates of CHO-K1 cell 2 L bioreactor fedbatch cultivations were performed and daily sampled for nLC-MS/MS proteomic analysis. Collected data from day 3 up to day 11 showed high Pearson correlation of 93.7 ± 4 % with ca. 2500 proteins quantified. The different growth phases were separated by principal component analysis and hierarchical clustering approaches. Subsequent statistical analysis revealed distinct protein profiles, where steady increase or decrease over time were the most prominent clusters. Fisher exact enrichment tests yielded in significantly enriched protein annotations which were successfully mapped to growth and metabolic changes during fedbatch cell cultivation. Major improvements in cellular and process understanding were achieved and yielded in the identification of promising new targets, like strong endogenous promotors, for cellular engineering and process optimization of this biopharmaceutical relevant cell line.

2021-01-25 | PXD018439 | Pride

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