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ProteomicsImproved MS-based proteomics by the reduction of isotopic composition in vivo
Reducing the isotopic composition of proteins in vivo improves in-depth, high resolution MS-based quantitative proteomics. We used U-[12C]-glucose as the metabolic precursor of all amino acids in yeast. This substantially increased the peptide monoisotopic ion intensity in bottom-up analyses, greatl...
ORGANISM(S): Candida albicans (Yeast) 
2017-08-24 | PXD005364 | Pride
Protein half-life [u-12c]-carbon source Candida albicans Bottom-up ms-based proteomics 
UnknownExpression of a rice chitinase gene in transgenic banana ('Gros Michel', AAA genome group) confers resistance to black leaf streak disease.
Not available
S-EPMC3525978 | biostudies-literature
ProteomicsNovel insights into quantitative proteomics from an innovative bottom-up Simple Light Isotope Metabolic (bSLIM) labeling data processing strategy
The Simple Light Isotope Metabolic labeling (SLIM-labeling) is an inovative method to quantify proteome variations based on an original in vivo labeling strategy. Heterotrophic cells grown on a U-[12C] sole source of carbon synthesize U-[12C]-amino acids which are incorporated into proteins giving r...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-02-15 | PXD021329 | Pride
Openms Data processing workflow Yeast In vivo metabolic labeling Light carbon isotope Quantitative proteomics 12c Knime 
ProteomicsTraining set - Novel insights into quantitative proteomics from an innovative bottom-up Simple Light Isotope Metabolic (bSLIM) labeling data processing strategy
The Simple Light Isotope Metabolic labeling (SLIM-labeling) is an inovative method to quantify proteome variations based on an original in vivo labeling strategy. Heterotrophic cells grown on a U-[12C] sole source of carbon synthesize U-[12C]-amino acids which are incorporated into proteins giving r...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-02-16 | PXD021502 | Pride
Openms Data processing workflow Yeast In vivo metabolic labeling Light carbon isotope Quantitative proteomics 12c Knime 
ProteomicsExtending the range of SLIM-labeling applications: from human cell lines in culture to Caenorhabditis elegans whole-organism labeling
The simple light isotope metabolic-labeling technique relies on the in-vivo biosynthesis of amino acids from U-[12C]-labeled molecules provided as the sole carbon source. The incorporation of the resulting U-[12C]-amino acids into proteins presents several key advantages for mass-spectrometry-based ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Caenorhabditis elegans 
2023-06-23 | PXD028880 | Pride
Auxin Mass spectrometry Bottom-up proteomics Human cell line Essential amino acids Slim metabolic labeling Caenorhabditis elegans 
TranscriptomicsTranscription profiling by array of human dendritic cells after Poly(I:C)-based or PGE2-based maturation
Generation of human monocyte-derived DCs Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll density centrifugation from buffy coats or whole blood of healthy donors and resuspended in serum-free medium (CellGro, CellGenix GmbH, Freiburg, Germany), supplemented with penicillin (50U/ml)...
ORGANISM(S): Homo sapiens 
2008-11-01 | E-MEXP-1230 | biostudies-arrayexpress
MetabolomicsCollected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research
MIADB: a cumulative collection of 172 tandem mass spectrometry (MS/MS) of a vast array of monoterpene indole alkaloids. Samples were analyzed using an Agilent LC-MS system composed of an Agilent 1260 Infinity HPLC coupled to an Agilent 6530 ESI-Q-TOF-MS operating in positive mode. A Sunfire analytic...
2018-12-03 | MTBLS142 | MetaboLights
TranscriptomicsGene profiling: U87 IRE1 dominant negative cells vs. U87ctrl cells in culture
Transcriptome analysis was performed from human U87 glioblastoma cell clones: U87 IRE1.NCK DN (U87dn, IRE1 dominant negative) and U87 control (U87ctrl, empty plasmid). Cells were grown in DMEM supplemented with 10% FBS and glutamine for 16 hours in culture prior mRNA isolation and analyses U87dn c...
ORGANISM(S): Homo sapiens 
2010-08-08 | E-GEOD-22385 | biostudies-arrayexpress
GenomicsSATAY sequencing data from multiple biological and technical replicates of Saccharomyces cerevisiae
Transposon insertion site sequencing (TIS) is a powerful tool that has significantly advanced our knowledge of functional genomics. While providing valuable insights, these applications of TIS focus on (conditional) gene essentiality and neglect possibly interesting but subtle differences in the imp...
ORGANISM(S): Saccharomyces cerevisiae 
2024-11-18 | E-MTAB-14476 | biostudies-arrayexpress
GenomicsGenome wide localization of Activation induced cytidine deaminase (AID), Spt5, and RNA Polymerase II (PolII) in mouse
Activation induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes. Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these key transactions little is kn...
ORGANISM(S): Mus musculus 
2010-10-05 | E-GEOD-24178 | biostudies-arrayexpress
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