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MetabolomicsAssessment of human plasma and urine sample preparation for re-producible and high-throughput UHPLC-MS clinical metabolic phenotyping

Clinical metabolic phenotyping employs metabolomics and lipidomics to detect and measure thousands of metabolites and lipids within human samples. This approach aims to identify metabolite and lipid changes between phenotypes (e.g. disease status) that aid understanding of biochemical mechanisms ...

2020-08-06 | MTBLS1465 | MetaboLights
TranscriptomicsTranscription profiling by array of mouse wild type and E-cadherin knockout embryonic stem cells grown with or without cytokine leukemia inhibitory factor
We previously observed that E-cadherin knockout embryonic stem cells do not differentiate in the absence of the cytokine leukemia inhibitory factor (LIF) (Soncin et al., 2009, Stem Cells 27 p2069-2080). This experiment was designed to compare the transcription profile of E-cadherin KO ES cells cultu...
ORGANISM(S): Mus musculus 
2011-06-19 | E-MEXP-2836 | biostudies-arrayexpress
MetabolomicsProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis

Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the...

2021-09-01 | MTBLS1903 | MetaboLights
TranscriptomicsscRNA-seq of human fetal lung explants with R-SPONDIN Inhibition and human fetal lung primary tissue
Here, we used single cell RNA-sequencing (scRNA-seq) to profile 13-week post-conception distal human fetal lung explants cultured in an air liquid interface system and treated with an LGR5 ectodomain adenovirus that inhibits R-Spondin function or control adenovirus. A third, non-infected, condition ...
ORGANISM(S): Homo sapiens 
2022-01-01 | E-MTAB-10662 | biostudies-arrayexpress
MetabolomicsVeterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs (T. congolense assay)

Livestock diseases caused by Trypanosoma congolense, T. vivax and T. brucei, collectively known as nagana, are responsible for billions of dollars in lost food production annually. There is an urgent need for novel therapeutics. Encouragingly, promising antitrypanosomal benzoxaboroles are under v...

2020-10-22 | MTBLS1309 | MetaboLights
ProteomicsSystematic analysis of the impact of R-methylation on RBPs-RNA interactions
RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization and interactions with other pro...
ORGANISM(S): Homo sapiens (Human) 
2021-08-25 | PXD024601 | Pride
Prmts Oops R-methylation Rbps 
ProteomicsE-selectin Affinity Glycoproteomics Reveals Neuroendocrine Proteins and the Secretin Receptor as a Poor Prognosis Signature in Colorectal Cancer
Colorectal cancer (CRC) cells express glycoproteins with sialylated Lewis antigens (sLe), crucial for metastasis via E-selectin binding. However, these glycoepitopes lack cancer specificity, and E-selectin-targeted glycoproteins are unknown. Here we established a framework for identifying metastasi...
ORGANISM(S): Homo sapiens (Human) 
2024-11-11 | PXD054727 | Pride
Cancer glycoproteome Colorectal cancer E-selectin Secretin receptor Metastasis 
TranscriptomicsRNA-seq of human intestinal organoids colonized with E. coli and other immature intestinal tissues
We performed RNA-seq to demonstrate that the epithelium of human pluripotent stem cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. RNA was isolated using the mir...
ORGANISM(S): Homo sapiens 
2017-09-01 | E-MTAB-5801 | biostudies-arrayexpress
MetabolomicsDeficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease
Non-alcoholic fatty liver is the most common liver disease worldwide. Here, we show that the mitochondrial protein mitofusin 2 (Mfn2) protects against liver disease. Reduced Mfn2 expression was detected in liver biopsies from patients with non-alcoholic steatohepatitis (NASH). Moreover, reduced Mfn2...
2018-01-25 | MTBLS600 | MetaboLights
ProteomicsTargeting ERAP enhances anti-tumor immunity by disrupting the NKG2A/HLA-E inhibitory checkpoint
New targets that enhance anti-tumor immunity must be identified to improve the efficacy of cancer immunotherapy. Here we show that loss of endoplasmic reticulum aminopeptidase (ERAP) family proteins improves anti-tumor immunity and synergizes with immune checkpoint blockade. Mechanistically, we show...
ORGANISM(S): Homo sapiens (Human) 
2024-11-21 | PXD052031 | Pride
Human Hla-e Orbitrap Immunotherapy 
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