Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk ATAC-seq of IL27 treated OT-1 cells

ABSTRACT: To better understand the mechanisms downstream of IL-27 signaling, we performed ATAC sequencing on repetitively stimulated OT-I T cells treated with IL-27.

INSTRUMENT(S): NextSeq 1000

ORGANISM(S): Mus musculus

SUBMITTER: Soren Muller

PROVIDER: E-MTAB-14584 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bulk RNA-seq OT-I Cd8 T cells

Project description:To better understand the mechanisms downstream of IL-27 signaling, we performed RNA sequencing on repetitively stimulated OT-I T cells treated with IL-27.

2024-12-06 | E-MTAB-14580 | biostudies-arrayexpress

Gene expression profile of influenza virus antigen-activated or in vitro stimulated murine CD8+ T cells on day 7

Project description:The precise timing and pathway of memory CD8+ T cells differentiation from naïve T cells have remained undetermined. We found the smaller cell-size and slower cell cycling cells were segregated from the proliferative larger cell-size activated T cell pool at the peak of infection. Gene signature of the smaller cell-size slower cycling cells and the large cell-size proliferative cells was compared to the signature of naïve, effector, central and effector memory CD8+ T cells. Total RNA samples were prepared from sorted populations of larger or smaller cell-sized cells from spleens of influenza virus PR8-OVA-infected mice on day 7 p.i. or from in vitro 7 days culture after stimulation with plate-bound anti-CD3ε (1.0 μg ml−1) and anti-CD28 mAb (0.5 μg ml−1). Effector T-cell control samples were prepared from SIINFEKL (100 ng ml−1) stimulated OT-I cells after 4 days of in vitro culture with rIL-2 (10 ng/ml) and sorted as CD8+CD44hiCD62Llo. Control bona fide effector memory and central memory T cells were sorted from the spleens of PR8-OVA-infected mice on day 42 p.i. Naive cells were sorted as CD8+CD44loCD62Lhi cells from uninfected C57BL/6 mice.

2015-02-25 | E-GEOD-48219 | biostudies-arrayexpress

Transcription profiling of mouse spleen after immunized using LPS vs MPL as adjuvant.

Project description:An unresolved issue in immunology is the extent to which inflammatory effects are needed for robust T cell responses. In this study, mice were immunized by iv injection using either high toxicity lipopolysaccharide (LPS) or low toxicity monophosphoryl lipid A (MPL) as adjuvant. Six hours after iv immunization, whole spleens were harvested and gene expression was measured in unfractionated splenic populations of cells. The analysis indicated that the low toxicity adjuvanticity of MPL was associated with TLR4-mediated signaling that was biased to the TRIF branch of TLR4, while LPS generated balanced MyD88 and TRIF-associated outcomes. Experiment Overall Design: B6.SJL mice adoptively transferred with T cells from B6.OTI and OTII transgenic TCR transgenic were immunized via intravenous injection with ova peptides alone ("Ova"), or with LPS ("OvaLPS") or MPL as adjuvant ("OvaMPL"). Six hours after immunization, the mice were euthanized by cervical dislocation, the spleens were removed and immediately lysed in guanidium chloride, and kept frozen until being used to extract total cellular RNA. Three mice each were given the indicated treatments, with independent processing and analysis of nine samples total.

2008-06-15 | E-GEOD-7768 | biostudies-arrayexpress

Translational repression of pre-formed cytokine mRNA prevents chronic activation of memory T cells

Project description:Memory T cells are critical to protect us from recurring infections. Their instantaneous reactivity to pathogens is empowered by persistent expression of cytokine mRNA. How aberrant protein production of this pre-formed mRNA is prevented in the absence of infection, however, remains unresolved. We show that protein production in memory T cells is blocked through a 3’untranslated region (3’UTR)-mediated process, and that AU-rich elements (AREs) are key herein. Germ-line deletion of AREs leads to chronic IFN- production in bona fide memory T cells. Strikingly, the aberrant protein production does not result from increased mRNA levels and/or half-life. Rather, AREs block the recruitment of cytokine mRNA to ribosomes, a process that is mediated by the ARE-binding protein ZFP36L2. Thus, AREs are crucial elements for translational repression that allow murine and human memory T cells to contain pre-formed cytokine mRNAs, while preventing undesirable protein production in the absence of infection.

2018-05-15 | PXD008051 | Pride

Memory CD8+ T cells require stress-levels of acetate for optimal function

Project description:How systemic metabolic alterations during acute infections impact immune-cell function remains poorly understood. Hess and colleagues demonstrate that acetate rapidly increases during infections, which drives acetylation of GAPDH in memory CD8+ T cells and thereby catalyzes the rapid recall response. Comparison of mRNA profile of control vs. 3d acetate exposed memory OT-I T cells

2016-05-18 | E-GEOD-79600 | biostudies-arrayexpress

Compartment resolved reference map from highly purified naive, activated, effector and memory CD8+ cells

Project description:Differentiation of CD8+ T lymphocytes into effector and memory cells is key for an adequate immune response and relies on complex interplay of pathways that convey signals from cell surface to nucleus. In this study, we fractionated four CD8+ T cell subtypes; naïve, recently activated effector, effector and memory cells into membrane, cytosol, soluble nucleus, chromatin-bound and cytoskeleton compartments. Using LC-MS/MS analysis, identified peptides were matched to human peptides/proteins (SwissProt). Compartment fractionation and gel-LC-MS separation identified 2399 proteins in total. Among these 735 were detected in all five, 241 in four, 257 in three, 368 in two and 798 found in only one fraction. Comparison between the two most different subsets, naïve and effector, yielded 146 significantly regulated proteins.

2015-02-04 | PXD001065 | Pride

Expression data from in vitro versus in vivo differentiated Th17 cells

Project description:In vitro differentiated Th17 have a distinct expression profile compared to in vivo differentiated Th17 Several conditions of Th17 cells were tested, with 2-3 replicates per condition.

2015-04-18 | E-GEOD-68017 | biostudies-arrayexpress

The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-17 | E-GEOD-49931 | biostudies-arrayexpress

De novo DNA methylation by DNA Methyltransferase 3a controls early effector CD8+ T cell fate decisions following activation

Project description:DNMT3a is a de novo DNA methyltransferase expressed robustly after T cell activation that regulates plasticity of CD4+ T cell cytokine expression. Here we show that DNMT3a is critical for directing early CD8+ T cell effector and memory fate decisions. While effector function of DNMT3a knockout T cells is normal, they develop more memory precursor and fewer terminal effector cells in a T cell intrinsic manner compared to wild-type animals. Rather than increasing plasticity of differentiated effector CD8+ T cells, loss of DNMT3a biases differentiation of early effector cells into memory precursor cells. This is attributed in part to ineffective repression of Tcf1 expression in knockout T cells, as DNMT3a localizes to the Tcf7 promoter and catalyzes its de novo methylation in early effector WT CD8+ T cells. This data identifies DNMT3a as a crucial regulator of CD8+ early effector cell differentiation and effector versus memory fate decisions. Examination of global genomic DNA methylation by MBD-seq in naÃ¯ve CD8 T cells and CD8 T cells 8 days post Vaccinia-Ova infection, comparing OT1 TCR-Tg CD8 T cells isolated from WT and T cell conditional DNMT3a KO mice.

2016-08-20 | E-GEOD-85823 | biostudies-arrayexpress

Transcriptional profile of carcinoma-stem-like cells (CSC) extracted from a primary ovarian cancer cell line

Project description:A population of non-adherent cells with stem-like characteristics (OVA-BS4 spheres) has been isolated from a primary human epithelial ovarian cancer (EOC) cell line (OVA-BS4) under selective conditions. OVA-BS4 spheres were characterized for their pharmacological properties and their molecular profile by microarray and RT-qPCR.

2018-01-15 | E-MTAB-4799 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data