Browse
Submit Data
Databases
API
Help

Dataset Information

255 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thermal proteome profiling of Jurkat cells

ABSTRACT: Determine melting temperature of proteins in Jurkats

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell

SUBMITTER: Maria Faelth Savitski

LAB HEAD: Marcus Bantscheff

PROVIDER: PXD008639 | Pride | 2018-05-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	01076_F1_R1_P0113360B02_TMT10.raw.gz	Raw
	01076_F1_R1_P0113360B03_TMT10.raw.gz	Raw
	01076_F1_R1_P0113360B04_TMT10.raw.gz	Raw
	01076_F1_R1_P0113360B05_TMT10.raw.gz	Raw
	01076_F1_R1_P0113360B06_TMT10.raw.gz	Raw

Items per page:

1 - 5 of 44

Publications

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Savitski Mikhail M MM Zinn Nico N Faelth-Savitski Maria M Poeckel Daniel D Gade Stephan S Becher Isabelle I Muelbaier Marcel M Wagner Anne J AJ Strohmer Katrin K Werner Thilo T Melchert Stephanie S Petretich Massimo M Rutkowska Anna A Vappiani Johanna J Franken Holger H Steidel Michael M Sweetman Gavain M GM Gilan Omer O Lam Enid Y N EYN Dawson Mark A MA Prinjha Rab K RK Grandi Paola P Bergamini Giovanna G Bantscheff Marcus M

Cell 20180315 1

Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed "multiplexed proteome dynamics profiling" (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of ...[more]

PMID: 29551266

Similar Datasets

Thermal proteome profiling of JQ1

Project description:Goal of this experiment was the identification of proteins affected in their thermal stability by JQ1.

2018-05-02 | PXD008638 | Pride

2 Dimensional Thermal proteome profiling of JQ1

Project description:Goal of this experiment was the identification of proteins affected dose dependently in their thermal stability by JQ1.

2018-05-02 | PXD008626 | Pride

FOXP3 binding sites in promoter regions of human Jurkat T cells

Project description:The transcription factor (TF) Forkhead Box P3 (FOXP3) is constitutively expressed in high levels in natural occurring CD4+CD25+ regulatory T cells (nTreg) and is not only the most accepted marker for that cell population, but is considered lineage determinative. Chromatin immunoprecipitation (ChIP) of transcription factors in combination with genomic tiling microarray analysis (ChIP-on-Chip) has been shown to be an appropriate tool to identify FOXP3 transcription factor binding sites (TFBS) on a genome-wide scale. In combination with microarray expression analysis the ChIP-on-Chip technique allows to identify direct FOXP3 target genes. ChIP-on-Chip analysis of human FOXP3M-NM-^T2 isoform expressed in resting and PMA / ionomycin stimulated Jurkat T cells revealed several thousand putative FOXP3 binding sites and importance of intronic regions for FOXP3 binding. Knowledge of general distribution patterns of FOXP3 TFBS in the human genome under resting and activated conditions contributes to a better understanding of this TF and its influence on direct target genes with importance for Treg cell phenotype and function. ChIP-DNA from FOXP3(M-NM-^T2) expressing Jurkat T cells under resting and PMA / ionomycin stimulated conditions from duplicate experiments was analyzed. FOXP3-specific tiling array data were analyzed in reference to an individual isotype control dataset (J-FOXP3 ChIP'd with FOXP3 antibody vs. J-FOXP3 ChIP'd with isotype control antibody). In total 8 tiling array analyses were performed (2x resting J-FOXP3 with FOXP3-IP, 2x resting J-FOXP3 with isotype-IP, 2x PMA/iono J-FOXP3 with FOXP3-IP, 2x PMA/iono J-FOXP3 with isotype-IP)

2012-11-26 | E-GEOD-37252 | biostudies-arrayexpress

Nonionic surfactants can modify the thermal stability of globular and membrane proteins interfering with the thermal proteome profiling principles to identify protein targets

Project description:The membrane proteins are essential targets to understand cellular function. The unbiased identification of membrane protein targets is still the bottleneck for a system- level understanding of cellular response to stimuli or perturbations. It has been suggested to enrich the soluble proteome with membrane proteins by introducing nonionic surfactants in the solubilization solution. This strategy was aiming to simultaneous identify the globular and membrane protein targets by thermal proteome profiling principles. However, the thermal shift assay would surpass the cloud point temperature from the nonionic surfactants most frequently utilized for membrane protein solubilization. It is expected that around the cloud point temperature, the surfactant micelles would suffer structural modifications altering the proteome solubility. Here, we show that the presence of nonionic surfactants can alter protein thermal stability from a mixed globular, and membrane proteome. In the presence of surfactant micelles, the changes in protein solubility analyzed after the thermal shift assay are affected by the thermal dependent modification of the micelles size, and their interaction with proteins. We demonstrate that the introduction of nonionic surfactants for the solubilization of membrane proteins is not compatible with the principles of target identification by thermal proteome profiling methodologies. Our results lead to explore thermal-independent strategies for membrane protein solubilization to assure confident membrane protein target identification. The proteome-wide thermal shift methods have already shown their capability to elucidate mechanism of actions from pharma, biomedicine, analytical chemistry, or toxicology and finding strategies, free from surfactants, to identify membrane protein targets would be the next challenge.

2023-03-20 | PXD037153 | Pride

Transcription profiling by array of human PMA-activated Jurkat cells

Project description:Cyclin T1-dependent genes in activated Jurkat cells. HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo. One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb. Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription. Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication. Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors. Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation. The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1. Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021). SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication. It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors. The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors. Experiment Overall Design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in activated Jurkat cells.

2008-10-20 | E-GEOD-10232 | biostudies-arrayexpress

Thermal proteome profiling of Arabidopsis thaliana

Project description:Six biological replicates of Arabidopsis thaliana were subjected to protein extraction, ten-temperature gradient precipitation, TMT labeling, off-line alkaline fractionation, and LC-MS/MS. The resulting data was used downstream for untargeted modeling of protein unfolding and melting temperature estimation.

2018-11-23 | PXD011200 | Pride

Multiplexed proteome dynamics profiling of HSP90 inhibitor 17-AAG

Project description:Investigation of proteostatic effects of HSP90 inhibition by 17-AAG and differentiation of maturation state dependent HSP90 requirements of proteins.

2018-04-05 | PXD008633 | Pride

Thermal proteome profiling of stationary-phase E. coli treated with semapimod

Project description:There is a need to discover and develop non-toxic antibiotics that are effective against metabolically dormant bacteria, which underlie chronic infections and promote antibiotic resistance. Traditional antibiotic discovery has historically favored compounds effective against actively metabolizing cells, a property that is not predictive of efficacy in metabolically inactive contexts. Here, we combine a stationary-phase screening method with deep learning-powered virtual screens and toxicity filtering to discover compounds with lethality against metabolically dormant bacteria and favorable toxicity profiles. The most potent and structurally novel compound without any obvious mechanistic liability was semapimod, an anti-inflammatory drug effective against stationary-phase E. coli and A. baumannii. Integrating microbiological assays, biochemical measurements, and single-cell microscopy, we show that semapimod selectively disrupts and permeabilizes the bacterial outer membrane by binding lipopolysaccharide. This work illustrates the value of harnessing non-traditional screening methods and deep learning models to identify non-toxic antibacterial compounds that are effective in infection-relevant contexts.

2023-08-21 | PXD044230 | Pride

A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance

Project description:Thermal Proteome Profiling (TPP) allows for identification of drug (off-)targets by evaluating shifts in apparent melting temperature for proteins. In this study, we use TPP to identify the targets for a novel antifolate (C1).

2023-08-08 | PXD040155 | Pride