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MetabolomicsInositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites
Vesicular traffic and membrane contact sites between organelles enable the exchange of proteins, lipids, and metabolites. Recruitment of membrane tethers to contact sites between the endoplasmic reticulum (ER) and the plasma membrane is often triggered by calcium. In contrast, we reveal here a funct...
2021-05-06 | MTBLS2444 | MetaboLights
MetabolomicsA paired transcriptomic, metabolomic and fruit-quality data resource from field-grown tomatoes across eight agricultural sites in Ningxia, China

Tomato fruit phenotypes are shaped by genotype, agronomic management and local environment, yet matched molecular and environmental datasets from commercial field settings remain scarce. Here we describe a paired resource comprising fruit transcriptomes, untargeted metabolomes, fruit-quality meas...

2026-09-14 | MTBLS15436 | MetaboLights
GenomicsDouble fragmentation ChIP-seq provides single nucleotide resolution Tcf4 binding characteristics
ChIP-seq has become the method of choice for studying functional DNA-protein interactions on a genome wide scale. The method is based on co-immunoprecipitation of DNA binding proteins with formaldehyde cross-linked DNA, followed by deep sequencing of immunoprecipitated chromatin fragments, allowing ...
ORGANISM(S): Homo sapiens 
2010-11-01 | E-GEOD-18481 | biostudies-arrayexpress
ProteomicsBenchmarking multiple fragmentation methods on an Orbitrap Fusion for top-down phospho-proteoform characterization
Top-down analysis of intact proteins by mass spectrometry provides an ideal platform for comprehensive proteoform characterization, in particular, for the identification and localization of post-translational modifications (PTM) co-occurring on a protein. One of the main bottlenecks in top-down prot...
ORGANISM(S): Homo sapiens (Human) 
2015-07-16 | PXD001845 | Pride
Fragmentation Bora Ethcd Top down proteomics Phosphorylation Proteoform Orbitrap fusion 
ProteomicsAn optimised fragmentation regime for cross-linking/mass spectrometry
In this study we compared three different fragmentation techniques and two combined fragmentation schemes available on a novel tribrid mass spectrometer (Orbitrap Fusion Lumos, Themro Fisher Scientific) CID, HCD, ETD, ETD with supplemental CID (ETciD) and ETD with supplemental HCD (EThcD) on cross-l...
ORGANISM(S): Homo sapiens (Human) 
2016-08-02 | PXD003737 | Pride
Etcid Cid Cross-linking Ethcd Hcd Etd 
GenomicsSequencing Apoptotic DNA Breakpoints
DNA fragmentation is a well-recognized hallmark of apoptosis. However, the precise DNA sequences cleaved during apoptosis triggered by distinct mechanisms remain unclear. We used next-generation sequencing of DNA fragments generated in Actinomycin D-treated human HL-60 leukemic cells to generate a h...
ORGANISM(S): Homo sapiens 
2011-10-15 | E-GEOD-32997 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide mapping of human Staufen1 binding sites
Purpose: We performed RNA-Immunoprecipitation in Tandem (RIPiT) experiments against human Staufen1 (Stau1) to identify its precise RNA binding sites in a transcriptome-wide manner. To monitor the consequences of Stau1 binding in terms of target mRNA levels and ribosome occupancy, we modified the lev...
ORGANISM(S): Homo sapiens 
2013-11-25 | E-GEOD-52447 | biostudies-arrayexpress
GenomicsGenome-wide cell-free DNA fragmentation in patients with cancer
Genome-wide cell-free DNA fragmentation in patients with cancer
PRJNA543357 | ENA
GenomicsGenome-wide cell-free DNA fragmentation in patients with cancer
Genome-wide cell-free DNA fragmentation in patients with cancer
PRJNA543358 | ENA
ProteomicsMass spectrometry characterization of light chain fragmentation sites in cardiac AL amyloidosis: insights into the timing of proteolysis
Amyloid fibrils are polymeric structures originating from aggregation of misfolded proteins. In vivo, proteolysis may modulate amyloidogenesis and fibril stability. In light chain (AL) amyloidosis, fragmented light chains (LCs) are abundant components of amyloid deposits; however, site and timing of...
ORGANISM(S): Homo sapiens (Human) 
2020-10-15 | PXD020858 | Pride
Proteolysis Mass spectrometry Amyloid fibrils Proteomics Cardiomyopathy 
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