Project description:Wnt Phospho protein profiling comparing control and Fto deficient cell after Wnt3a stimulation Control vs Fto deficient MEFs treated with Wnt 3a condioned medium for 40 minutes. 6 replicates per array

2013-11-21 | E-GEOD-52572 | biostudies-arrayexpress

Transcription profiling of primary human astrocytes from brain treated by stathmin, poly IC and ultrapure LPS to examine the effects of different Toll-like receptor agonists

Project description:Goal of the experiment was to examine the effects of different Toll-like receptor agonists on the human astrocyte response, in termsof levels of transcripts encoding cytokines, chemokines and theirreceptors. Stathmin and poly IC are considered as agonist for TLR3, LPSas an agonist for TLR4. The manuscript we are about to submit to Journal of Immunology contains these data, and identifies stathmin, aprotein, as a novel TLR3 agonist. We all know that poly IC is, and bycomparing the transcript responses in astrocytes to either poly IC andstathmin, and observing the similarity in these responses, the experiment adds to the evidence that stathmin indeed activates a verysimilar cellular response as poly IC. The LPS-induced response,mediated by TLR4, is included as a reference, to illustrate thatanother TLR-mediated reaction produces quite something different.

2010-02-11 | E-TABM-851 | biostudies-arrayexpress

Multiplexed interactome analysis reveals the molecular architecture of the human prefoldin network

Project description:The majority of proteins are organized in protein complexes. Protein complexes represent an important cellular organizational layer, which regulate and catalyze most of the cellular processes. Within the field of proteomics several techniques such as Affinity Purification (AP) and co-fractionation (co-Frac) coupled to mass spectrometry (MS) were developed in order to study protein complexes. Our approach, deep interactome profiling coupled to MS (DIP-MS), is a combination of the benefits of these approaches by combining the selectivity of AP-MS together with a blue native-page size-based fractionation, in order to deconvolute the co-purified complexes, in which the bait is a constitutive subunit. To ensure high-quality quantitation along the fractionation gradient, and to keep data acquisition time limited, we developed a high-throughput (HT) sample preparation method and high-throughput data independent acquisition (DIA) method, enabling us to acquire almost one co-Frac gradient per day. Additionally, a tailored machine learning approach was devised – protein-protein interaction prophet (PPIprophet) which enabled the scoring of the co-elution proteins to retrieve PPIs respectively protein complexes. The method was employed to depict the complex modularity within the prefoldin and prefoldin-like protein complexes, allowing us to I) describe protein complex isoforms, II) derive stoichiometries and abundance distributions of co-purified complexes and III) identify reported and new client proteins and client complexes of the PAQosome, a multi-subunit co-chaperone complex, necessary for the stabilization and formation of multiple complexes such as the RNA polymerases (RNA Pol I, RNA Pol II, RNA Pol III). This study thereby demonstrates the applicability of our method and shows it strength and sensitivity by depicting the prefoldin complexes within only a single experiment.

2024-03-11 | PXD035032 | Pride

human hTERT-RPE1 cell spheroid : Control siRNA transfected vs. YAP1 siRNA transfected

Project description:Transcriptional profiling of human hTERT-RPE1 cell spheroids comparing Control siRNA transfected hTERT-RPE1 cell spheroids with those transfected with YAP1 siRNA. Two-condition experiment, Control siRNA vs.YAP1 siRNA hTERT-RPE1 cell spheroids. Biological replicates: 1 Control siRNA, 1YAP1 siRNA transfected, independently grown and harvested. Bothreplicates per array.

2015-02-01 | E-GEOD-54146 | biostudies-arrayexpress

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