Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2985260.fastq.gz | Fastqsanger.gz | |||
| ERR2985270.fastq.gz | Fastqsanger.gz | |||
| ERR2985261.fastq.gz | Fastqsanger.gz | |||
| ERR2985271.fastq.gz | Fastqsanger.gz | |||
| ERR2985262.fastq.gz | Fastqsanger.gz |
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Project description:The generation of CD8+ T-cell memory is an important aim of immunization. While several distinct subsets of CD8+ T-cell memory have been described, the lineage relationships between effector (EFF), effector memory (EM) and central memory (CM) T cells remain contentious. Specifically, there is contradictory experimental evidence to support both the linear (Naive>EFF>EM>CM) and progressive differentiation (Naive>CM>EM>EFF) models. In this study, we applied a systems biology approach to examine global transcriptional relationships between the three major CD8+ T cell subsets arising endogenously as a result of vaccination with three different prime-boost vaccine regimens. Differential gene expression analysis and principle component analysis revealed that central memory cells were more closely related to naive T cells than both effector memory and effector cells. When the transcriptional relationships between subsets were enriched in an unbiased fashion with known global transcriptional changes that result when T-cells repeatedly encounter antigen, our analysis favored a model whereby cumulative antigenic stimulation drives differentiation specifically from Naive > CM > EM > EFF. These findings provide an insight into the lineage relationship between mature CD8+ T-cell subsets and will help in the rational design of vaccines aimed at generating effective immune responses against infections and cancer. Effector (EFF), effector memory (EM), central memory (CM) and naive CD8+ T cells from mice spleen. Memory subset arise endogenously as a result of vaccination with three different prime-boost vaccine regimens: DNA-rAd5, rAd5-rAd5 and rAd5-rLCMV.
2013-08-01 | E-GEOD-42459 | biostudies-arrayexpress
Project description:Chromatin insulators demarcate the genome into distinct transcriptional domains and contribute to higher-order genome organization. In Drosophila, Su(Hw), CP190, and Mod(mdg4)67.2 are core protein components of the gypsy insulator complex. Multimerization of these core components contributes to formation of large structures within the nucleus termed insulator bodies. Post-translational modifications of insulator proteins appear to affect insulator body localization and be required for full insulator activity, but few factors involved in these processes have been identified. To address this gap in understanding, we performed a high-throughput visual screen for Mod(mdg4)67.2-GFP localization using a ubiquitination-related RNAi library. We identified ubiquitination pathway proteins Effete (Eff) and Cullin 4 (Cul4), as novel regulators of CP190 localization and function. Both Eff and Cul4 physically associate with gypsy insulator proteins and promote gypsy-dependent insulator barrier activity. Moreover, Cul4 extensively colocalizes with CP190 on chromatin and assists in the recruitment of CP190 to gypsy sites. Both Eff and Cul4 affect transcription near topologically associating domain (TAD) borders, with Eff specifically altering the 3D nuclear positioning of gypsy insulator sites. Overall, our findings reveal a novel role for ubiquitination pathway-related enzymes in chromatin insulator activity, 3D genome organization, and gene expression.
2026-02-27 | GSE243452 | GEO
Project description:Tissue nanotransfection (TNT) based topical electrophoretic delivery of Etv2, Foxc2, and Fli1 (EFF) plasmids achieve induced vasculogenesis (iV) in the skin by inducing vasculogenic fibroblasts (VF). scRNA-seq analysis revealed TET-dependent gain of VF in dermal fibroblasts in response to EFF. Emergence of VF required TET-dependent demethylation of fibroblast-borne endothelial genes in vivo. Fibroblast-specific inducible overexpression of EFF in TARGATT mice caused induction of TET1/2/3, followed by transition of fibroblast to VF in vivo. TET induction was associated with elevated 5-hmC abundance in VF. TET-dependent demethylation of fibroblast-borne endothelial genes caused the formation of VF and rescued perfusion in diabetic ischemic limbs. TNTEFF rescued perfusion and closure of diabetic wounds. TET enzymes, suppressed in diabetics, play a pivotal role in causing endogenous EFF-induced VF state change of skin fibroblasts. TNT delivery of EFF transcription factors upregulate TET expression. This work is the first to recognize the significance of TET in the inducible formation of blood vessels to rescue diabetic ischemic tissue.
2024-12-05 | GSE268094 | GEO
Project description:Understanding the molecular mechanisms of feed efficiency is an important step toward sustainability of salmonids aquaculture. In this study, the liver and white muscle proteomes of efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) farmed in sea water were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach. In total, 2,746 liver and 702 white muscle quantified proteins were compared between 21 EFF and 22 INEFF fish. Protein synthesis was enriched in both liver and white muscle of the EFF group while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. The SOM in the INEFF group was significantly higher than EFF fish showing INEFF fish probably was the dominant group. The INEFF group (dominant) suffered stress and shifted to consume energy through protein catabolism. As the first study, the results provide a preliminary picture of the fundamental molecular landscape of feed efficiency in Chinook salmon farmed in sea water
2023-04-27 | PXD028025 | Pride