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ProteomicsProtein turnover rates under high light treatment
To characterize Arabidopsis proteomics and transcritomics changes in response to high light treatment. We quantify specific transcipts and protein abundance changes under both control and high light stress conditions. We aim to investigate the causality and interconnection of transcription and pr...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2022-05-05 | PXD010889 | Pride
Arabidopsis High light 13c partial labelling Shoot 
TranscriptomicsGut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids
Acetate, propionate and butyrate are the main short-chain fatty acids (SCFAs) that arise from the fermentation of fibers by the colonic microbiota. While many studies focus on the regulatory role of SCFAs, their quantitative role as a catabolic or anabolic substrate for the host has received relativ...
ORGANISM(S): Mus musculus 
2013-10-21 | E-GEOD-45926 | biostudies-arrayexpress
TranscriptomicsHepatic gene expression during liver regeneration in response to partial hepatectomy: late time points (24h, 38h, 48h)
The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the “priming” phase, in which cytokines TNF-a and IL-6 activate their respective receptors in...
ORGANISM(S): Mus musculus 
2011-02-16 | E-GEOD-20426 | biostudies-arrayexpress
ProteomicspyQms - partial labeled proteome gold standard
" The novel mass spectrometry quantitation tool pyQms can calculate isotope patterns for molecules that have any isotope enrichment or combinations of, e.g. 13C or 15N and allows partially labeled molecules to be quantified as well, as observed in pulse or pulse-chase experiments where enrichment le...
ORGANISM(S): Chlamydomonas reinhardtii 
2017-08-10 | PXD003236 | Pride
Lc-ms/ms Gold standard dataset 
TranscriptomicsHepatic gene expression during liver regeneration in response to partial hepatectomy: early time points (0.5h,1h,2h,4h)
The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the “priming” phase, in which cytokines TNF-a and IL-6 activate their respective receptors in...
ORGANISM(S): Mus musculus 
2011-02-16 | E-GEOD-20425 | biostudies-arrayexpress
ProteomicsA Collision-induced Dissociation Cleavable Isobaric Tag for Peptide Fragment Ion-based Quantification in Proteomics
Fragment ion-based proteome quantification methods quantify peptides based on unique peptide fragment ions avoiding the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a novel approach that relies on a collision-induced dissoci...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-08-17 | PXD018790 | Pride
Isotopic labelling Proteomics Cid cleavable tag Fragment ion-based quantification Isobaric labelling 
ProteomicsEBprot: Bayesian Analysis of Labelling-based Quantitative Proteomics Data
Labelling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs) between biological samples. The current data analysis platform relies on protein-level ratios, where peptide-level ratios are averaged to yield a single summary ratio for each protein. In shotgu...
ORGANISM(S): Homo sapiens (Human) 
2015-06-29 | PXD001426 | Pride
Hierarchical mixture model Quantitative analysis Stable isotope labelling Differential expression 
TranscriptomicsGene Expression in the Human Mammary Epithelium in response to consumption of high fat (H-FAT) and high carbohdyrate (H-CHO) diets.
Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. We hypothesized that de novo lipogenesis, as reflected by incorporation of 13C carbons from [U-13C]glucose into fatty acids (FAs) and glycerol in triglycerides (TG), will be greate...
ORGANISM(S): Homo sapiens 
2014-05-19 | E-GEOD-51874 | biostudies-arrayexpress
ProteomicsProteomics of biphenyl labelling study
protein based stable isotope probing was performed for identifying microorganisms actually responsible for biphenyl biodegradation in soil environment.
ORGANISM(S): soil metagenome 
2022-02-16 | PXD023646 | Pride
Soil 13c-labelled peptides 
ProteomicsBasement membrane turnover and circulating matrix biomarkers in kidney disease
Chronic kidney disease (CKD) is characterised by kidney fibrosis and represents a major public health concern. Alport syndrome, a common monogenic cause of kidney failure caused by genetic variants in the type IV collagen genes COL4A3, COL4A4 or COL4A5, leads to abnormal basement membrane remodellin...
ORGANISM(S): Mus musculus (Mouse) 
2026-05-21 | PXD067091 | Pride
Ecm Kidney Alports Turnover 
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