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

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

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Alzbeta Chabronova

LAB HEAD: Mandy Peffers

PROVIDER: PXD046111 | Pride | 2024-05-22

REPOSITORIES: Pride

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			Action	DRS
	PC1.mgf	Mgf
	PC1.mzid.gz	Mzid
	PC1.raw	Raw
	PC2.mgf	Mgf
	PC2.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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Secretome of SW1353 cells cultured in the presence of the 10 ng/ml TGF-β3

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

2024-05-22 | PXD046109 | 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

Proteomic profiles of synovial fluids derived from autologous chondrocyte implantation surgery

Project description:The pathology of failure in currently used biological treatments (cell therapies and microfracture) for cartilage repair or early osteoarthritis (OA) is poorly understood. We aimed to identify a reliable panel of biological predictors, present in synovial fluid, which can be used in the preoperative setting to optimise patient selection and therapy efficacy. The-long term aim is to reduce the number of patients who progress to end-stage OA and require knee replacement by making earlier, less invasive treatments more effective. In this first stage, we have taken synovial fluid aspirates from patients undergoing autologous chondrocyte implantation (ACI) at our centre in Oswestry, UK. Synovial fluids (SFs) were obtained from 14 ACI responders (mean Lysholm improvement of 33 (17-54)) and 13 non-responders (mean Lysholm decrease of 14 (4-46)) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Dynamic range compression of synovial fluids coupled with label-free quantification mass spectrometry (MS), was used in an unbiased approach to identify predictive markers of ACI success or failure and to investigate the biological pathways involved in the clinical response to ACI.

2017-07-04 | PXD005220 | Pride

RNA-seq of human monocyte derived macrophages exposed to different atherogenic compounds

Project description:The accumulation of lipid-laden macrophages (foam cells) in the arterial wall is a crucial early step in atherosclerotic plaque development. Modified low-density lipoprotein (LDL) is the primary cholesterol source for foam cells, taken up in an unregulated manner through scavenger receptors. This type of cells exhibit reduced migratory capacity while producing elevated levels of pro-inflammatory cytokines, thereby promoting inflammation and plaque progression. Still our understanding of the transcriptomic changes during macrophage-to-foam cell conversion remains limited. In this experiment, we aimed to identify genes responsible for the accumulation of cholesterol in human monocyte-derived macrophages exposed to modified and native LDL. The monocyte samples collected from healthy individuals were purified and exposed to modified and native LDLs obtained from plasm of atherosclerotic patients. RNA extracted after 24h of incubation was sequenced with polyA selection. The resulting data was normalised with limma and undergone DEG analysis followed by upstream analysis workflow with TRANSPATH and TRANSFAC databases to discover master regulator molecules.

2023-08-14 | E-MTAB-13261 | 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

mRNA-Seq of head tissue from Doa and fne mutants, Drosophila melanogaster.

Project description:Transcriptional profiling of head tissue of Drosophila Darkener of apricot (Doa) and found in neurons (fne) mutants was performed by RNA-SEQ in females and males. The transcriptional and post-transcriptional targets of these genes, which are involved in regulation by several processes including splicing and mRNA stability, are examined and compared to wild-type. Examination of mRNA profiles in heads of wild-type male and female adult flies are compared to mutant

2014-03-13 | E-GEOD-37811 | biostudies-arrayexpress

Ethanol Exposure during Differentiation of Human Induced Pluripotent Stem Cells Reduces Cardiomyocyte Generation and Alters Metabolism

Project description:In this study, we investigated the effects of ethanol exposure on cardiomyocyte differentiation by treating the cells with various concentrations of ethanol. The results indicated that ethanol exposure during hiPSC-CM differentiation reduced cell viability, cell proliferation, and cardiomyocyte yield, and caused mitochondrial dysfunction, redox imbalance, and changes of proteomic profiles.

2025-05-23 | PXD056092 | Pride

Irisin is a Pro-Myogenic Factor that Induces Skeletal Muscle Hypertrophy and Rescues Denervation-Induced Atrophy

Project description:C2C12 myoblasts were seeded at a density of 25,000 cells/cm2 in a 10cm cell culture dish and differentiated with low serum differentiation medium at 37 °C, 5% CO2 for 72h and further treated with either DB or recombinant Irisin protein (1000ng/ml) for 6h, 12h, 24h and 48h. Myotubes were resuspended in 2ml of TRIzol ® for each 10cm dish and RNA isolation was performed according to the manufacturer s protocol. Purified isolated RNA was then subjected to Illumina bead array sequencing and data analysis, as per in-house protocols (Sciencewerke, Singapore). Only genes that were upregulated or downregulated by 1.5-fold were considered significant. For genes that had multiple probes (with different accession number), only one probe with the highest upregulation or downregulation was taken into consideration.

2017-09-11 | E-MTAB-6024 | biostudies-arrayexpress

RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (Promoter)

Project description:A study to define the binding loci of RelA-containing NF-kappaB dimers in a human myometrial smooth muscle cell line after exposure to TNF. Monolayers of PHM1-31 cells were exposed to TNF (10ng/ml) for 1 hour or left unstimulated. The Chromatin immunoprecipitation (ChIP) assay was performed to recover RelA-bound chromatin or non-specifically bound chromatin with IgG. That chromatin was prepared and used to probe Affymetrix GeneChIP 1.0R Human Promoter arrays. Three biological replicates of each experiment were conducted. Datasets were subsequently analysed in Partek Genomics Suite V6.6 where baseline was normalised by subtraction of IgG values from conrresponding RelA-immunoprecipitated samples. Control samples immunoprecipitated with RelA were then compared with TNF-stimulated samples immunoprecipitated with RelA.

2015-03-31 | E-GEOD-65690 | biostudies-arrayexpress

Terbutyl stress mRNA

Project description:mRNA amount analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course Transcriptomic analysis of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.

2008-05-23 | E-GEOD-9645 | biostudies-arrayexpress

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