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MetabolomicsA microfluidics-based in vitro model of the gastrointestinal human-microbe interface
Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human–microbial crosstalk), w...
2017-07-28 | MTBLS328 | MetaboLights
TranscriptomicsTranscription profiling of neutrophils isolated by microfluidics: Clinical Microfluidics for Neutrophil Genomics and Proteomics
Neutrophils play critical roles in modulating the immune response. However, neutrophils have a short circulating half life, are readily stimulated in vitro, and have low levels of cellular mRNA when compared to other blood leukocyte populations. All of these factors have made it difficult to evaluat...
ORGANISM(S): Homo sapiens 
2010-06-16 | E-GEOD-22103 | biostudies-arrayexpress
ProteomicsA microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics
Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications, especially for personalized cancer immunotherapies. However, the current experimental approach to extract HLA-I-restricted peptides requires a bulky sample source, which remai...
ORGANISM(S): Homo sapiens (Human) 
2023-05-12 | PXD040858 | Pride
Mass spectrometry Immunopeptidomics Sample preparation Data-independent acquisition Automation Microfluidics 
TranscriptomicsHigh-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics
The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High...
ORGANISM(S): Mus musculus 
2015-06-05 | E-GEOD-62050 | biostudies-arrayexpress
TranscriptomicsInducible defense response of C. cinerea against its fungiverous nematode A. avenae in microfluidics device
The fungal toxin-encoding genes are highly upregulated in the vegetative mycelium upon challenge with the predator. Our recent studies in microfluidics have shown that latter induction is spatially restricted to parts of the vegetative mycelium that is in direct contact with the predator. In order t...
ORGANISM(S): Coprinopsis cinerea 
2018-11-30 | E-MTAB-7005 | biostudies-arrayexpress
ProteomicsHigh-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning
We develop a parallel flow projection and transfer learning-based spatial proteomics framework that combines microfluidics and a deep neutral network.
ORGANISM(S): Homo Sapiens Rattus Norvegicus Mus Musculus 
2025-01-15 | PXD045687 |
ProteomicsMiniaturized sample preparation on a digital microfluidics device for sensitive bottom-up microproteomics of mammalian cells using magnetic beads and mass spectrometry-compatible surfactants
We used digital microfluidics (DMF) for the sample preparation of approximately 100 mammalian cells, and subsequent bottom-up proteome analysis by LC-MS. This comprised optimization of cell lysis conditions for DMF, the development of detergent-buffer systems, and adaptation of the single-pot, solid...
ORGANISM(S): Homo sapiens (Human) 
2019-10-07 | PXD014158 | Pride
Digital microfluidics Detergents Sp3 Microproteomics Miniaturization 
ProteomicsImplementation of microfluidics for antimicrobial susceptibility assays: issues and optimization requirements
Despite the continuous emergence of multi-drug resistant pathogens, the number of new antimicrobials reaching the market is critically low. Natural product peptides are a rich source of bioactive compounds, and advances in mass spectrometry have achieved unprecedented capabilities for the discovery ...
ORGANISM(S): Viola inconspicua 
2020-09-04 | PXD020857 | Pride
Microfluidics Antimicrobial susceptibility testing Viola 
ProteomicsImmunopeptidomics by use of a microfluidics chip.
A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementatio...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD022194 | Pride
Human Bladder cancer Ligandome Patient derived organoid Hla-i Renal cell carcinoma Microfluidics Ovarian cancer Immunopeptidome Jy cell line Chip Mhc-i Rcc 
ProteomicsCombination of digital microfluidics and magnetic bead-based intact proteoform elution for top-down nanoproteomics of single C. elegans
While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up LC-MS workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we here established a facile one-pot sample preparation protocol bas...
ORGANISM(S): Caenorhabditis elegans 
2023-06-19 | PXD039883 | Pride
Top-down proteomics  nanoproteomics  caenorhabditis elegans  digital microfluidics 
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