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Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function. VLDLHDL corona

ABSTRACT: The MS data set contains the result from HDL VLDL corona used in the publication, titled Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Kai Liu

LAB HEAD: Kai Liu

PROVIDER: PXD041944 | Pride | 2023-06-07

REPOSITORIES: Pride

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Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function. Rat Plasma

Project description:The MS data set contains the result from each individual rat plasma used in the publication, titled Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function.

2023-06-07 | PXD041925 | Pride

Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function. Individual corona

Project description:The MS data set contains the result from each individual rat plasma derived corona used in the publication, titled Multiomics analysis of naturally efficacious LNP coronas reveals high-density lipoprotein is necessary for LNP function.

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Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress

Comparative analysis of the human and mouse placental transcriptome and proteome

Project description:An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. Over 7,000 orthologs were detected with 70% co-expressed and over 80% of genes known to cause placental phenotypes in mouse were co-expressed. These genes form a tight protein-protein interaction network with novel candidate genes likely to be important in placental structure and/or function. The entire data is available as a web-accessible database to guide the informed development of mouse models to study human disease This experiment is now fully represented in NCBI Peptidome database with accession PSE115; http://www.ncbi.nlm.nih.gov/peptidome/search/index.shtml?acc=PSE115 Microdissection of human villous trees and mouse placental labyrinth. Tissues were split for microarray and protein analysis. For protein analysis samples were first fractionated by differential sucrose gradients into mitochrondria, cytosol, microsomes and nuclei. Mitochrondira and neuclei were each extracted by two different methods for soluble and insoluble material. Each subcellular fraction for each tissue was analysed in quintuplet by 9 step 2 dimensional LC/MSMS. This generated a total of 270 mzXML files for each tissue.

2009-06-29 | E-GEOD-13299 | biostudies-arrayexpress

A screen of Campylobacter jejuni protein microarrays with antisera to identify immunogenic proteins

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2018-12-29 | E-MTAB-7535 | biostudies-arrayexpress

In situ Analysis of Nanoparticle Soft Corona and Dynamic Evolution

Project description:How soft corona i.e., the protein corona’s outer layer contributes to “biological” identity of nanomaterials (NMs) is largely unknown due to a longstanding challenge in capturing protein composition of the soft corona in situ. We herein develop an in situ “Fishing” method that can monitor the dynamic formation of protein corona on ultra-small chiral Cu2S nanoparticles (NPs) allowing us to directly separate and identify their protein composition. This method can detect spatiotemporal processes in the evolution of hard and soft coronas on chiral NPs, revealing subtle differences in their composition even within several minutes. This study highlights the importance of in situ and dynamic analysis of soft/hard corona composition, provides detailed insights into the roles of protein corona composition in mediating the biological responses of NPs, and offers a universal strategy to characterize the soft corona that will serve as a powerful tool for rational design of biomedical NMs.

2022-10-13 | PXD033976 | Pride

Insulin-Like Growth Factor Receptor 1 and Mammalian Target Of Rapamycin Blockade: Novel Mechanisms of Resistance and Synergistic Drug Combinations for Ewing Sarcoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-01 | E-GEOD-78124 | biostudies-arrayexpress

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2015-05-12 | E-GEOD-68764 | biostudies-arrayexpress

Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 TFs

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2010-01-08 | E-GEOD-19198 | biostudies-arrayexpress

Salivary cytokine alterations in HIV infection

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2011-09-08 | E-GEOD-24411 | biostudies-arrayexpress

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