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One-pot analysis on cyclosporine A binding

ABSTRACT: Investigate if one-pot analysis works on several energetic-based proteomics method on cyclosporine A.

INSTRUMENT(S): Orbitrap Fusion Lumos

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

SUBMITTER: Baiyi Quan

LAB HEAD: Michael C. Fitzgerald

PROVIDER: PXD014309 | Pride | 2021-09-08

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	CPP_Y_CsA_1Pot_Run1.raw	Raw
	CPP_Y_CsA_1Pot_Run2.raw	Raw
	CPP_Y_CsA_1Pot_Run3.raw	Raw
	CPP_onepot.msf	Msf
	SPROX_EN_Y_CsA_1Pot_Run1.raw	Raw

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1 - 5 of 16

Publications

Comparative Analysis of Mass-Spectrometry-Based Proteomic Methods for Protein Target Discovery Using a One-Pot Approach.

Cabrera Aurora A Wiebelhaus Nancy N Quan Baiyi B Ma Renze R Meng He H Fitzgerald Michael C MC

Journal of the American Society for Mass Spectrometry 20191122 2

Recently, several mass-spectrometry- and protein-denaturation-based proteomic methods have been developed to facilitate protein target discovery efforts in drug mode-of-action studies. These methods, which include the stability of proteins from rates of oxidation (SPROX), pulse proteolysis (PP), chemical denaturation and protein precipitation (CPP), and thermal proteome profiling (TPP) techniques, have been used in an increasing number of applications in recent years. However, while the advantag ...[more]

PMID: 32031398

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One-pot comparative analysis and characterization of young and old mice brain lysates

Project description:A comparison of different energetics based techniques for the characterization of young and old mice brain cell lysates. The techniques of stability of proteins from rates of oxidation (SPROX), thermal proteome profiling (TPP), Limited Proteolysis (LiP) and conventional expression level analyses were compared and the relative advantages and disadvantages are discussed.

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One-pot comparative analysis and characterization of MCF-7 and MCF-10A cell lines

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2023-02-22 | PXD036268 | Pride

Cyclosporine on fibroblast

Project description:To elucidate the gene profile of anti-fibroproliferative effects of cyclosporine, we added TGF-b and/or CsA to MRC5 (fetal human lung fibroblast) cell line. After 24 hours serum starvation, fibroblasts were treated with 3 ng/ml TGF-β1 and were treated with or without 2μg/ml Cyclosporine and effects were examined at 48 hours after treatment. Expression of three genes (IGFBP3, ID1 and PPARG) from this signature was quantified in the same RNA samples by real-time PCR. TGF-β and cyclosporine induced gene expression data was measured in MRC5 (fetal human fibroblast cell line) at 48h after treatments. The dose of TGF-β was 3 ng/ml and cyclosporine was 2 μg/ml. The comparison was done between four groups (control, TGF-β, cyclosporine and TGF-β plus cyclosporine).Three independent experiments were performed at each treatments using different samples for each experiment.

2010-11-09 | E-GEOD-25200 | biostudies-arrayexpress

Utilization of Stability-based Proteomics for the Investigation of Structured RNA-protein Interactions

Project description:The stability of proteins from rates of oxidation (SPROX), thermal protein profiling (TPP) methods as well as triple helix pulldowns with LC-MS/MS readouts are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU) in LNCaP nuclear lysate. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.

2024-01-31 | PXD043878 | Pride

Metal-induced Protein Precipitation in E. coli

Project description:Using a range of copper we have utilized Metal-induced Protein Precipitaiton (MiPP) technique to elucidate the copper midpoints of the proteins found in an E. coli proteome. Using bottem-up proteomics techniques and TMT-10 plex isobaric mass-tags we were able to use MiPP to classify proteins based off of their sensitivity to copper.

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Cyclosporine on fibroblast

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Cyclosporine A timecourse 0, 12, 48 hours

Project description:Effect of 4.2 micromolar Cyclosporine A on human renal proximal tubular cell line HK-2 over 48 hours Keywords: time-course

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Low dose ruxolitinib plus cyclosporine to treat murine immune-mediated bone marrow failure

Project description:Background and methods: Ruxolitinib (RUX), a Jak1/2 inhibitor, has been reported to attenuate murine bone marrow failure recently. Its potential toxocicty of anemia and thrombocytopenia in human remains a concern. To minimize its potential toxoxicity, we tested therapeutic effectsof low dose ruxolitinib plus cyclosporine in murine model of immune-mediated bone marrow failure. Bone marrow CD8 and CD4 T cells were sorted from treated or untreated bone marrow failure mice. RNA-Seq and analysis was performed using SMART-Seq mRNA LP Kit (Takara) and the Illumina Novaseq6000, according to the Institute's protocols. Results: low dose of ruxolitinib plus cyclosporine improved pancytopenia and BM cellularity and decreased BM T cell infiltration in bone marrow failure mice. RNA sequencing demonstrated that low dose of ruxolitinib plus cyclosporine suppressed immune-related pathways in bone marrow infiltrated CD8 T cells and MHC-II expression in CD4 T cells compared with untreated mice. Conclusion: Our results demonstrate that low dose of ruxolitinib plus cyclosporine remains the efficacy in attenuation of disease and extending survival of immune-mediated bone marrow failure mice.

2024-05-08 | GSE240864 | GEO

Effect of hypoxia and treatment with cyclosporine A on chemotaxis of RAMOS B cells

Project description:To investigate the effect of changes in oxygen tension and treatment with cyclosporine A on the chemotactic migration of B cells, we grew RAMOS B cells at 19% and 1% oxygen levels, and at 19% and 1% oxygen levels after treatment with cyclosporine A. We then performed RNA-seq on these RAMOS B cells and subequently gene expression profiling analysis on this RNA-seq data.

2023-02-13 | GSE212853 | GEO

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