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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression profiling of IL6 and Myc TG mouse plasmacytoma

ABSTRACT: To identify differentially expressed genes in mouse IL6 and Myc double TG plasmacytoma, total RNAs from mouse plasmacytoma generated from IL6 + Myc TG mice were applied to NIAID mouse gene expression arrays. The transcriptome in IL6+ Myc TG mouse PCT was compared to transcriptome in IL6 TG mouse PCT Eleven set of IL6+Myc TG PCTs and ten set of IL6 TG PCTs were used. Total RNAs from each mouse labelled with Cy3, and reference RNAs labeled with Cy5 were hybridzed to spotted oligomicroarray.

ORGANISM(S): Mus musculus

SUBMITTER: Wendy DuBois

PROVIDER: E-GEOD-19336 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression profiling of IL6 and Myc TG mouse plasmacytoma

Project description:To identify differentially expressed genes in mouse IL6 and Myc double TG plasmacytoma, total RNAs from mouse plasmacytoma generated from IL6 + Myc TG mice were applied to NIAID mouse gene expression arrays. The transcriptome in IL6+ Myc TG mouse PCT was compared to transcriptome in IL6 TG mouse PCT

2010-02-01 | GSE19336 | GEO

PCT and normal

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2010-05-19 | E-GEOD-12157 | biostudies-arrayexpress

Mus musculus

Project description:Expression profiling of IL6 and Myc TG mouse plasmacytoma

| PRJNA121705 | ENA

PCT and normal

2008-09-30 | GSE12157 | GEO

Testing TMT-SPS-MS3 and label free approach in recalcitrant Mago (Mangifera indica L.) peel tissues

Project description:Significant progress has been observed in recent years in proteomics tools. However, minimal application of the newest proteomic tools has been massively applied in plant recalcitrant tissues in non-model fruits. This constant occurrence constrains the progress in understanding essential molecular processes during postharvest shelf life (PSL) of fleshy fruits. In fact, comparative proteomic studies in fruit like mango, guava, papaya, and avocado are minimal. Therefore, we set up a label free quantitation (LFQ) and TMT-SPS-MS3 pipeline for comparative study of mango peels during PSL. Our protocol included different protein extraction and peptide fractionation before mass spectrometry analysis. In doing so we were able to confidently identify 4,400 proteins with high confidence, among which 1087 were differentially accumulated. The combination of phenolic protein extraction, high-pH reverse-phase peptide fractionation and LFQ exhibited the best approach for relative quantification, but other protein extraction, peptide fractionation and data acquisition showed significant complementation. LFQ and Byonic also allowed the determination of intact N-glyco peptides on proteins such as the desiccation-related protein, which molecular dynamics analysis support the occurrence of N-glycans providing stability of the protein. Our study represents the first massive proteomics comparison of mango peels during PSL.

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Proteomics analysis of monocyte-derived hepatocyte-like cells identifies integrin beta 3 as a specific biomarker for drug-induced liver injury by diclofenac

Project description:Idiosyncratic drug-induced liver injury (iDILI) is a major cause of acute liver failure resulting in liver transplantation or death. Prediction and diagnosis of iDILI remain a great challenge, as current models provide unsatisfying results in terms of sensitivity, specificity and prognostic value. The absence of appropriate tools for iDILI detection also impairs the development of reliable biomarkers. Here, we report on a new method for identification of drug-specific biomarkers. We combined the advantages of monocyte-derived hepatocyte-like (MH) cells, able to mimic individual characteristics, with those of a novel mass spectrometry (MS)-based proteomics technology to assess potential biomarkers for Diclofenac-induced DILI. We found over 2700 proteins differentially regulated in MH cells derived from individual patients. Herefrom, we identified integrin beta 3 (ITGB3) to be specifically upregulated in Diclofenac-treated MH cells from Diclofenac-DILI patients compared to control groups. Finally, we validated ITGB3 by flow cytometry analysis of whole blood and histological staining of liver biopsies derived from patients diagnosed with Diclofenac-DILI. In summary, our results show that biomarker candidates can be identified by proteomics analysis of MH cells. Application of this method to a broader range of drugs in the future will exploit its full potential for the development of drug-specific biomarkers.

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Expression profiling of BORIS knockout mice testis

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Identification of myelin basic protein interactome using TurboID proximity labeling proteomics

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