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MetabolomicsCreation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti
Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approa...
2021-03-17 | MTBLS576 | MetaboLights
MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
MetabolomicsLipid Data Analyzer: The LDA algorithm against the in silico library LipidBlast (LipidBlast benchmarking experiment)
Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectr...
2017-11-07 | MTBLS397 | MetaboLights
ProteomicsA hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in triple negative breast cancer (TNBC) tissues. Primary tumor tissue lysates from 105 TNBC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, were used to generate...
ORGANISM(S): Homo sapiens (Human) 
2024-05-31 | PXD047793 | Pride
Proteomics Mass spectrometry Data independent acquisition Assay library Triple-negative breast cancer 
TranscriptomicsHybrid Mimics and Hybrid Vigor in Arabidopsis (F4 data)
F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1€“like phenotype, we have by...
ORGANISM(S): Arabidopsis thaliana 
2015-08-17 | E-GEOD-64740 | biostudies-arrayexpress
TranscriptomicsSmall RNAs as important regulators for the hybrid vigour of super-hybrid rice
Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature ...
ORGANISM(S): Oryza sativa 
2014-08-17 | E-GEOD-51468 | biostudies-arrayexpress
ProteomicsHigh-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics
Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge...
ORGANISM(S): Morganella Morganii Clostridium Butyricum Lactobacillus Acidophilus Enterococcus Faecalis Feces Metagenome Enterobacter Asburiae Pseudomonas Aeruginosa 
2023-07-19 | PXD043890 |
TranscriptomicsHybrid Mimics and Hybrid Vigor in Arabidopsis (F6 data)
F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have ...
ORGANISM(S): Arabidopsis thaliana 
2015-08-17 | E-GEOD-64742 | biostudies-arrayexpress
ProteomicsComprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer
The zebrafish (Danio rerio) retina has been increasingly used for studying vertebrate visual processing and ocular growth regulation as it has a high anatomical and physiological similarity to the human eye. Recently, the integration of trapped ion mobility spectrometry (TIMS) with parallel accumula...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2026-06-17 | PXD076440 | Pride
Dia Retina Zebrafish Dda 
GenomicsDevelopment and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system
Development and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system
PRJNA359495 | ENA
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