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ProteomicsIdentification of salicylic acid (SA)- and pathogen-responsive ubiquitin-binding proteins in Arabidopsis thaliana
The ubiquitin-proteasome system (UPS) is a key regulatory mechanism in plant immunity. Target proteins are labelled with ubiquitin chains that form distinct topological structures to modulate their activity and stability. Here, we identified ubiquitin-binding proteins (UBPs) that specifically intera...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2026-02-12 | PXD071198 | Pride
ProteomicsA pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease
Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA. Nat Biotechnol. 2011, 29(7):635-43. doi: 10.1038/nbt.1899. PMCID:PMC3366591. Discovery, AIMS, and MRM datasets Discovery_Tranche_hash: b/quYtp/Q8fY...
2013-12-19 | MSV000078513 | MassIVE
TranscriptomicsUnique gene program of rat mesenteric arteries as revealed by Deep RNA Sequencing
This study used Deep RNA sequencing to define gene expression in the small resistance arteries and compare to a reference conduit artery, the aorta Methods: Deep RNA Sequencing (~90 million reads) was performed on 2 samples of adult SD rat mesenteric arteries and compared to that of 2 samples of aor...
ORGANISM(S): Rattus norvegicus 
2015-07-13 | E-GEOD-64450 | biostudies-arrayexpress
ProteomicsAutocatalytic activation of a malarial egress protease is druggable and requires a protein cofactor
Malaria parasite egress from host erythrocytes (RBCs) is regulated by discharge of a parasite serine protease called SUB1 into the parasitophorous vacuole (PV). There, SUB1 activates a PV-resident cysteine protease called SERA6, enabling host RBC rupture through SERA6-mediated degradation of the RBC...
ORGANISM(S): Plasmodium falciparum (isolate 3D7) 
2021-03-16 | PXD024084 | Pride
Lc-msms Malaria Protease Sub1 Sera6 
TranscriptomicsGene expression changes with induction of in-vitro platinum-resistance in ovarian cancer cell lines.
We treated 8 human ovarian cancer cell lines with cisplatin in treatment/recovery cycles to induce in-vitro resistance to the drug. Microarrays measured gene expression at baseline and after each dose schedule (after recovery). OVCA cells lines (T8, OVCAR5, OV2008, IGROV1, C13, A2780S, A2780CP, and ...
ORGANISM(S): Homo sapiens 
2011-10-02 | E-GEOD-23553 | biostudies-arrayexpress
GenomicsH4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription
Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previo...
ORGANISM(S): Homo sapiens 
2015-05-02 | E-GEOD-65886 | biostudies-arrayexpress
MetabolomicsPlasma Lipidomics Identifies Anticedent Memory Impairment in Older Adults
Alzheimer's disease causes a progressive dementia that currently affects over 35 million individuals worldwide and is expected to affect 115 million by 2050 (ref. 1). There are no cures or disease-modifying therapies, and this may be due to our inability to detect the disease before it has progresse...
2014-03-09 | MTBLS72 | MetaboLights
ProteomicsIdentification of GLI-associated proteins by mass spectrometry
The Hedgehog signaling pathway is essential for the maintenance and response of several types of stem cells. To study the transcriptional response of stem cells to HH signaling, we searched for proteins binding to GLI proteins, the transcriptional effectors of the HH pathway in mouse embryonic stem ...
ORGANISM(S): Mus musculus (Mouse) 
2016-02-04 | PXD002494 | Pride
Nanog Embryonic stem cells Gli Hedgehog signaling 
ProteomicsDirected evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy
Enzymes that oxidize aromatic substrates have shown utility in a range of cell-based technologies including live cell proximity labeling (PL) and electron microscopy (EM), but are associated with drawbacks such as the need for toxic H2O2. Here, we explore laccases as a novel enzyme class for PL and ...
ORGANISM(S): Homo sapiens (Human) 
2025-04-12 | PXD062870 | Pride
Tmt Proximity labeling 
ProteomicsSpecter - Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
These data cover all of the analyses described in the paper "Specter: linear deconvolution as a new paradigm for targeted analysis of data-independent acquisition mass spectrometry proteomics". Specifically, the data consist of - 20 DIA and DDA files from the HEK293T/synthetic phosphopeptides spike-...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2018-03-19 | PXD006722 | Pride
Proteomics Data-independent acquisition 
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