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MetabolomicsMetabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants
Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr)...
2014-02-07 | MTBLS36 | MetaboLights
TranscriptomicsSpliced synthetic genes as internal controls in RNA sequencing experiments.
RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We h...
ORGANISM(S): synthetic construct Homo sapiens 
2016-07-21 | GSE77072 | GEO
MetabolomicsTroubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts
Metabolomics, understood as the science that manages the study of compounds from the metabolism, is an essential tool for deciphering metabolic changes in disease. The experiments rely on the use of high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-...
2019-12-12 | MTBLS1133 | MetaboLights
ProteomicsExtended multiplexing of TMT labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue
Age-related and/or high caloric intake driven changes in visceral adipose tissue contribute to the development of diabetes and cardiovascular disease. The lack of reliable, high-throughput methods to analyze the adipose tissue protein composition has limited our understanding of the protein network...
ORGANISM(S): Mus musculus (Mouse) 
2017-03-27 | PXD005953 | Pride
Protein expression Low fat diet Mudpit Proteomics Internal reference scaling normalization High fat diet Mouse Extended multiplexing Epididymal adipose tissue Aging Tandem mass tags Orbitrap fusion 
ProteomicsComBat HarmonizR enables the integrated analysis of independently generated proteomic datasets through data harmonization with appropriate handling of missing values
The integration of proteomic datasets, generated by non-cooperating laboratories using different LC-MS/MS setups can overcome limitations in statistically underpowered sample cohorts but has not been demonstrated to this day. In proteomics, differences in sample preservation and preparation strateg...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2022-05-23 | PXD027467 | Pride
Swath Metastudy Missing values Dda Dia Tmt Data integration Ffpe Silac Tissue Harmonisazion Fresh-frozen Combat 
GenomicsSpliced synthetic genes as internal controls in RNA sequencing experiments.
Spliced synthetic genes as internal controls in RNA sequencing experiments.
PRJNA309391 | ENA
MetabolomicsUntargeted Plasma Metabolomic Profiling of Parkinson’s Disease
Untargeted LC–MS metabolomic profiling was performed on plasma samples from a discovery cohort comprising 50 patients with Parkinson’s disease and 50 healthy controls. The study aimed to characterize disease-associated metabolic alterations, identify dysregulated metabolic pathways, and investigate ...
2026-09-03 | MTBLS15433 | MetaboLights
TranscriptomicsSpliced synthetic genes as internal controls in RNA sequencing experiments.
RNA sequencing (RNAseq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNAseq analysis. We hav...
ORGANISM(S): Homo sapiens 
2016-07-21 | E-GEOD-77072 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of S. cerevisiae rnt1 mutant and wild type cultures
Strain background is BMA64 with RNT1 gene deleted with the TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; A...
ORGANISM(S): Saccharomyces cerevisiae 
2007-07-07 | E-GEOD-2683 | biostudies-arrayexpress
ProteomicsThe Amniotic Fluid Proteome Changes Across Gestation in Humans and Rhesus Macaques
Amniotic fluid is a complex biological medium that offers mechanical protection and nutrition to the fetus, and also plays a key role in normal fetal growth, organogenesis, and potentially fetal programming. Amniotic fluid is also critically involved in longitudinally shaping the in utero milieu dur...
ORGANISM(S): Homo sapiens (Human) Macaca mulatta (Rhesus macaque) 
2023-10-24 | PXD043519 | Pride
Rhesus macaque Isobaric labeling Pregnancy Amniotic fluid Quantitative proteomics 
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