TNF induced gene expression in CD8 single positive thymocytes
Ontology highlight
ABSTRACT:
INSTRUMENT(S): BD FACSAira, Not applicable, Macintosh desktop, Illumina Genome Analyzer IIx
ORGANISM(S): Mus musculus
SUBMITTER: Louise Webb
PROVIDER: E-MTAB-4786 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:It is known that ubiquitination is important for T cell receptor (TCR) signaling during T cell activation but the breadth of ubiquitination events triggered during TCR signaling is not completely understood. This dataset utilizes di-glycine remnant profiling combined with mass spectrometry to identify a global landscape of ubiquitination events downstream of the TCR and to quantify changes ubiquitin abundance in response to TCR stimulation. Additionally, whole cell proteomics data were generated to measure protein abundances during TCR stimulation. Mouse primary T cells were isolated, proliferated and either remained resting or stimulated with CD3/CD28 to activate downstream signaling through the TCR and co-stimulatory pathways. Di-glycine remnant profiling and whole cell proteomics was performed on rested cells and cells that had undergone CD3/CD28 TCR stimulation for 4 hours. These data were analyzed to identify the ubiquitination events during TCR activation and to quantify the change in peptide-based ubiquitin abundance and total protein abundance over the course of the 4 hour TCR stimulation. Integration of di-glycine and whole cell proteomics was used to generate protein-specific predictions of whether ubiquitination events downstream of TCR signaling lead to a decrease in associated protein abundance. The analysis of these data suggests that T cell activation leads to an increase in ubiquitination that is not associated with proteasomal or lysosomal degradation.
2019-05-09 | PXD012831 | Pride
Project description:Themis1, a recently described T-lineage specific protein, is essential for thymic positive and negative selection. Although Themis1 has been clearly identified as a component of the T cell antigen receptor (TCR) signalosome, its precise role in TCR signaling remains unclear. Here, we used quantitative proteomic and TCR signaling reporter mice to gain insight into Themis1 signaling function. Mass spectrometry analysis of the Themis1 interactome identified Grb2, SHP1 and Vav1 as the principal interacting partners of Themis1 in thymocytes. The dataset contains mass spectrometry results from the analysis of 6 different kind of AP-MS purifications (based on immunoprecipitation using a Themis1 antibody) starting from the following samples: - thymocytes from WT mice, non stimulated (noted WT NS) - thymocytes from WT mice, stimulated with pervanadate (noted WT P) - thymocytes from GRB2 +/- mice (with decreased expression of GRB2), non stimulated (noted GRB2 NS) - thymocytes from GRB2 +/- mice (with decreased expression of GRB2), stimulated with pervanadate (noted GRB2 P) - thymocytes from Themis1 -/- mice (knock-out for Themis1), non stimulated (noted KO NS) - thymocytes from Themis1 -/- mice (knock-out for Themis1), stimulated with pervanadate (noted KO P) Three biological replicates were prepared for these 6 different conditions (noted, 1,2,3), yielding 18 analyzed samples. Three technical nanoLC-MS runs were acquired for each sample (noted R1, R2, R3), leading to the 54 nanoLC-MS raw files contained in the dataset.
2017-02-06 | PXD004072 | Pride
Project description:CD5 is characterized as an inhibitory co-receptor with important regulatory role during T cell development. To study the molecular mechanism by which CD5 operates, we used quantitative mass spectrometry to analyze the components of the CD5 signaling machinery in primary T cells. In a first set of experiments, CD5-containing complexes were immunoprecipitated from thymocytes of wild-type (WT) C57BL/6 mice. Thymocytes were treated with pervanadate to induce widespread activation of protein tyrosine kinases. Corresponding samples prepared from thymocytes of Cd5−/− mice were used as controls, to discriminate CD5-binding molecules from the background of contaminant proteins. Eight biological replicates were prepared for both conditions, and samples were analyzed in duplicate LC-MS runs. This first set of experiment is presented in TableS1 of the paper, and is associated to the MaxQuant result file “Interactome WT” in the present PX dataset. We analyzed the CD5 interactome at different time of stimulation with pervanadate (1min and 10min) using thymocytes from wild-type (WT) C57BL/6 mice. Corresponding samples prepared from thymocytes of Cd5−/− mice were used as controls. Three biological replicates were prepared for both conditions (WT and KO) and each time point (1min and 10min). This set of experiments is presented in TableS2 of the paper and is associated to the MaxQuant result file “Interactome at 1min and 10min” in the present PX dataset. We checked that the activation of CD5 (phosphorylation sites) and the formation of the signaling complex was comparable in different stimulatory conditions (comparison of WT thymocytes stimulated with either pervanadate or anti-CD3+anti-CD4 antibodies). We also analyzed the binding of CD5 interactors in thymocytes from a c-Cbl-/- mouse model (comparison of WT and c-Cbl-/-thymocytes stimulated with pervanadate). These experiments and the associated experimental design of the comparisons are summarized in TableS3 of the paper, and are based on the MaxQuant result file “Comparison of different stimulatory conditions” in this dataset. To check the phosphorylation status of the CD5 tyrosine residues at different time of stimulation, we analyzed samples immunoprecipitated from thymocytes of wild-type (WT) C57BL/6 mice, following stimulation with anti-CD3+anti-CD4 antibodies for 1min, 3min and 10min. This set of experiment is presented in TableS4 of the paper and is associated to the MaxQuant result file “CD5 pY kinetics” in the present PX dataset. To determine the role of Y429 in the context of CD5 signaling, we expressed a wild-type (CD5tgWt) or a mutated form of CD5, containing a tyrosine to phenylalanine substitution at position 429 (CD5tgY429F) in transgenic mice. We analyzed the CD5 interactome by comparing samples immunoprecipitated from thymocytes of these 2 mice models (following pervanadate stimulation, 6 and 5 biological replicates respectively) with samples prepared in the same way from Cd5−/− mice as controls (6 biological replicates). The results are shown in TableS5 of the paper, and correspond to the MaxQuant result file “interactome CD5tgWt_CD5tgY429F”.
2020-05-18 | PXD017343 | Pride
Project description:It has been previously described that in glioblastoma (GBM), BMPs deplete the tumorigenic potential of glioblastoma stem cells (GSCs), promoting their differentiation towards the astrocytic lineage. To gain more insight on how BMPs regulate differentiation in GSCs, we are interested in identifying new BMP target genes in GBM cells. To this end, the patient derived glioblastoma cell lines U3031MG and U3034MG were stimulated or not with 30ng/ml BMP7 for 2 and 24 h, total RNA was isolated from three biological replicates per condition, and a microarray screen with the Affymetrix U133plus2 platform was performed.
2021-05-01 | E-MTAB-9811 | biostudies-arrayexpress
Project description:A comparative RNA-SEQ analysis of control total RNA preparations from pooled E14.5 dorsal root ganglia was carried out to determine the performance of the RNAseq reactions at differing concentrations (3ng, 10ng & 30ng in high or low volumes) and concordance among different institutions using the same source of RNA. RNA was extracted from E14.5 dorsal root ganglia dissected from wild type C57BL/6J embryos and sequenced using Illumina Hiseq 2500 platform.
2014-12-15 | E-GEOD-63143 | biostudies-arrayexpress
Project description:Homologous recombination (HR) is crucial for genetic exchange, accurate repair of DNA double-strand breaks and pivotal for genome integrity. HR uses homologous sequences for repair, but how homology search, the exploration of the genome for homologous DNA sequences, is conducted in the nucleus remains poorly understood. Here, we use time-resolved chromatin immunoprecipitations of repair proteins to monitor homology search in vivo. We found that homology search proceeds by a probing mechanism, which commences around the break and samples preferentially on the broken chromosome. However, elements thought to instruct chromosome loops mediate homology search shortcuts, and centromeres, which cluster within the nucleus, may facilitate homology search on other chromosomes. Our study thus revealed crucial parameters for homology search in vivo and emphasizes the importance of linear distance, chromosome architecture and proximity for recombination efficiency. 2 new custom ChIP-chip platforms used; both Nimblegen; differ in oligo density: (platform 1: 2006-07-18_Scerevisiae_ChIP_Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array Version 1) ( platform 2: 100304_Scer2_MS_Chip_Stefan Jentsch MPI Biochemistry S.cerevisiae 135K Tiling Array Version 2) ChIP-chip profiling of DSB repair factors (Rad51, Rad52, RPA, gamma-H2A) upon single inducible DSBs in S.cerevisiae
2013-03-21 | E-GEOD-44844 | biostudies-arrayexpress
Project description:Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.
2021-02-12 | GSE110483 | GEO
Project description:The purpose of this study is to investigate certain genes inuduced/reduced by NK150460, novel compound possessing antitumor activity. To identify genes, time course samples were prepared from NK150460 sensitive and insensitive breast cancer cell lines. By comparing patterns in both sensitive and resistant cell lines, we tried to identify genes specifically modulated by NK150460 treatment. Four breast cance cell lines (3 sensitive cell lines, 1 insensitive cell line) were treated with NK150460 in vitro. 0, 3, 6, 24 hr after drug addition, total RNA were prepared. In total, 16 samples were prepared and subjected to microarray analysis.
2014-09-19 | E-GEOD-61548 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE34934: Expression data from BDC2.5 TCR Tg, preselected Rag-/-.B6 and Rag-/-.NOD.H2b thymocytes upon antigenic stimulation GSE34935: Expression data from BDC2.5 TCR Tg thymocytes on B6g7 and NOD background Refer to individual Series
2012-01-10 | E-GEOD-34936 | biostudies-arrayexpress
Project description:This series contain time course microarray data from MCF10A-Myc cells treated with either ethanol or Dexamethasone for 30 min, 2 hr, 4 hr, and 24 hr. This series contains three biological replicates that were analyzed as independent replicate experiments (data were normalized within each replicate experiment, not across all samples). Keywords: time course MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with either vehicle (ethanol) or Dex (10-6 M) for 0.5, 2, 4 or 24 hrs. Total RNA from each sample was extracted using QiagenM-bM-^@M-^Ys RNeasy Kit. Preparation of biotinylated cRNA and hybridization to oligonucleotide arrays (Affymetrix human genome genechip HG-U133A) were performed at the University of Chicago Microarray Core Facility. HG-U133A genechip contains 22,215 probe sets that represent approximately 16,000 human genes. The complete procedure was repeated independently three times. Gene chips were scanned and analyzed using Robust Multi-array Average (RMA) algorithm.
2006-06-01 | E-GEOD-4917 | biostudies-arrayexpress