Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative mass spectrometry-based proteomics reveals the dynamic protein landscape during initiation of human Th17 cell polarization

ABSTRACT: Quantitative mass spectrometry-based proteomics reveals the dynamic protein landscape during initiation of human Th17 cell polarization

PROVIDER: PRJNA487597 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7747370.fastq.gz	Fastqsanger.gz
	SRR7747371.fastq.gz	Fastqsanger.gz
	SRR7747372.fastq.gz	Fastqsanger.gz
	SRR7747373.fastq.gz	Fastqsanger.gz
	SRR7747374.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Quantitative mass spectrometry-based proteomics reveals the dynamic protein landscape during initiation of human Th17 cell polarization

Project description:CD4+ T cells play a key role in the adaptive immune system. Their subset, Th17 cells contribute to pathogenesis of inflammatory and autoimmune diseases and cancer. To reveal the Th17 cell-specific proteomic signature regulating Th17 cell differentiation and function in human we used a label-free mass spectrometry-based approach. To determine the degree of similarities and differences between the transcript and the protein levels, we performed a comprehensive analysis of the transcript-protein relationships. Comparison of the proteomics and RNA-sequencing data generated in this study during human Th17 differentiation revealed a high degree of overlap between the datasets. However, we found very limited overlap between the proteins differentially regulated in response to Th17 differentiation in human and mouse. Of the 758 and 397 proteins differentially regulated at 72h during Th17 specification in human and in mouse, respectively, only 33 were detected as differentially regulated in a similar fashion in both species. We validated a panel of selected proteins with known and unknown functions. Finally, using RNA interference (RNAi), we showed that SATB1 negatively regulates of human Th17 cell differentiation. To our knowledge, this study is the first to illustrate a comprehensive picture of the global protein landscape during early human Th17 cell differentiation. Poor overlap with recently reported mouse data underlines the importance of human studies for translational research.

2018-12-14 | GSE118974 | GEO

MMP qualitative and quantitative mass spectrometry

Project description:Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). The S40 and S2 strains were grown in 14N and 15N media with acetate separately. A biological replicate was made by switching the media. Mass spectrometry based quantitative proteomics were done on the mixtures to investigate the differences in expression patterns between S40 and S2. Keywords: isotope labeling mass spectrometry, quantitative proteomics

2005-09-20 | GSE2744 | GEO

Cyanobacterial identification by native mass spectrometry

Project description:Cyanobacterial identification by native mass spectrometry

| PRJEB45336 | ENA

pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase

Project description:Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of hematologic malignancies. It was shown that IMiDs impart gain of function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKFZ1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. Using a pulse-chase SILAC mass spectrometry-based proteomics approach, we demonstrate that lenalidomide induces the ubiquitination and degradation of ZFP91. We establish that ZFP91 is a bona fide IMiD dependent CRL4CRBN substrate and further show that ZFP91 harbors a zinc finger (ZnF) motif, related to the IKZF1/3 ZnF, critical for IMiD dependent CRBN binding. These findings demonstrate that single time point pulse-chase SILAC mass spectrometry-based proteomics (pSILAC-MS) is a sensitive approach for target identification of small molecules inducing selective protein degradation.

2017-03-01 | GSE94728 | GEO

Th17 polarization under hypoxia

Project description:Analysis of Th17 polarization under different oxygen concentrations and environmental toxin exposure at gene expression level. Results provide important information of the response of CD4+ T cells to low oxygen , such as genes involved in metabolism, transcriptional factor, up- or down-regulated specific cellular functions.

2017-06-01 | GSE90882 | GEO

Chromatin proteins linked to dosage compensation in Drosophila captured by ChIP-mass spectrometry

Project description:We report the usage of ChIP-mass spectrometry in identifying proteins and histone modifications involved in Drosophila dosage compensation. We identified a chromatin targeting factor, CG4747, that is involved in recognition of H3K36me3 and robust recruitment of the Drosophila MSL complex to its correct targets on the male X chromosome. ChIP-seq with PAP antibody of Drosophila larvae expressing C-terminally TAP-tagged CG4747.

2012-11-06 | E-GEOD-42025 | biostudies-arrayexpress

Gene array for identifying molecules involved in IL-10 regulation during Th17 polarization

Project description:IL-10 production by Th17 cells is critical for limiting autoimmunity and inflammatory responses. Gene array analysis on Stat6 and T-bet double deficient Th17 cells identified the Th2 transcription factor c-Maf to be synergistically up-regulated by IL-6 plus TGFbeta, and associated with Th17 IL-10 production. Both c-Maf and IL-10 induction during Th17 polarization depended on Stat3, but not Stat6 or Stat1, and mechanistically differed from IL-10 regulation by Th2 or IL-27 signals. TGFbeta was also synergistic with IL-27 to induce c-Maf, and induced Stat1 independent IL-10 expression in contrast to IL-27 alone. Retroviral transduction of c-Maf was able to induce IL-10 expression in Stat6 deficient CD4 and CD8 T cells, and c-Maf directly transactivated IL-10 gene expression through binding to a MARE motif in the IL-10 promoter. Together, these data reveal a novel role for c-Maf in regulating T effector development, and suggest that TGFbeta may antagonize Th17 immunity by IL-10 production through c-Maf induction. Our recent studies showed that IL-6 combined with TGFbeta differed from IL-6 combined with IL-23 for IL-10 production and pathogenic activities in CD4 T cells deficient in Stat6 and T-bet, despite similar IL-17 production. We performed gene array analysis on Stat6 and T-bet double deficient cells. We rationalized that by comparing gene expression in cells treated with IL-6 plus TGFbeta versus TGFbeta alone, we would be able to identify genes specific for standard Th17 polarization, and responsible for both IL-17 and IL-10 expression. By next comparing gene expression in cells treated with IL-6 plus TGFbeta versus IL-6 plus IL-23, we could eliminate molecules involved solely in IL-17 regulation, and obtain genes specifically responsible for IL-10 regulation.

2009-03-03 | E-GEOD-15029 | biostudies-arrayexpress

Optimal settings of mass spectrometry open search strategy for higher confidence

Project description:Optimal settings of mass spectrometry open search strategy for higher confidence

| PRJNA448556 | ENA

Differential Peptide Subtraction (DPS): mass spectrometry for human cancer virus discovery

Project description:Differential Peptide Subtraction (DPS): mass spectrometry for human cancer virus discovery

| PRJNA662225 | ENA

Chromatin proteins linked to dosage compensation in Drosophila captured by ChIP-mass spectrometry

2012-11-06 | GSE42025 | GEO