Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA119767 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Eos expression in Treg cells have been documented by several microarrays including ours. We hypothesized that Eos facilitates Foxp3- dependent gene repression in Regulatory T cells. In order to investigate the role of Eos in mediating the Foxp3-dependent gene silencing program, we utilized lentiviral shRNA knockdown of Eos in natural Tregs isolated from the periphery of Balb/C mice. A renilla luciferase (RL) gene specific shRNA lentivirus was used as a control for the transduction of cells. The transcriptional profile of naive T cells, natural Tregs, Eos knockdown Tregs, and control shRNA knockdown Tregs was compared using Agilent 4x 44K whole mouse genome array. The goal of this microarray is to document the global effect of the loss of Eos expression on the transcriptional profile of natrual Treg cells. Experiment Overall Design: Eos knock-down (si-Eos) was mediated by Lentivirus expressing GFP as a reporter of transduction and sorting marker. Renilla luciferase specific shRNA lentiviral transduction was carried out in parallel as a control. Naïve (CD4+CD25-CD62Lhi) T cells and nTreg cells were freshly isolated from Balb/C mice.
2009-10-16 | E-GEOD-17166 | biostudies-arrayexpress
Project description:Cellular binary fate decisions require the progeny to silence genes associated with the alternative fate. The major subsets of alpha:beta T cells have been extensively studied as a model system for fate decisions. While the transcription factor RUNX3 is required for the initiation of Cd4 silencing in CD8 T cell progenitors, it is not required to maintain the silencing of Cd4 and other helper T lineage genes. The other runt domain containing protein, RUNX1, silences Cd4 in an earlier T cell progenitor, but this silencing is reversed whereas the gene silencing after RUNX3 expression is not reverse. Therefore, we hypothesized that RUNX3 and not RUNX1 recruits other factors that maintains the silencing of helper T lineage genes in CD8 T cells. To this end, we performed a proteomics screen of RUNX1 and RUNX3 to determine candidate silencing factors.
2019-11-12 | PXD007511 | Pride
Project description:Eos expression in Treg cells have been documented by several microarrays including ours. We hypothesized that Eos facilitates Foxp3- dependent gene repression in Regulatory T cells. In order to investigate the role of Eos in mediating the Foxp3-dependent gene silencing program, we utilized lentiviral shRNA knockdown of Eos in natural Tregs isolated from the periphery of Balb/C mice. A renilla luciferase (RL) gene specific shRNA lentivirus was used as a control for the transduction of cells. The transcriptional profile of naive T cells, natural Tregs, Eos knockdown Tregs, and control shRNA knockdown Tregs was compared using Agilent 4x 44K whole mouse genome array. The goal of this microarray is to document the global effect of the loss of Eos expression on the transcriptional profile of natrual Treg cells.
2009-09-01 | GSE17166 | GEO
Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of deficiency of candidate FoxP3 cofactors (Xbp1, Eos, Gata1) on the expression of the Treg transcriptional signature, gene expression profiles were generated from purified splenic CD4+CD25hi Tregs of these mutant or knockout mice and their wildtype littermates.
2012-08-23 | E-GEOD-40273 | biostudies-arrayexpress
Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of FoxP3 and its candidate cofactors (Eos, Gata1, Helios, Irf4, Lef1, Satb1, Xbp1) on the expression of the Treg transcriptional signature, CD4+ conventional T cells (Tconv) activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding FOXP3, candidate TFs, or a combination of FOXP3 and candidate TFs. After 3 days in culture, the transduced cells were sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.
2012-08-23 | E-GEOD-40274 | biostudies-arrayexpress
Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. To study the impact of the combination of two transcription factors on the expression of the Treg transcriptional signature, CD4+ Tconv cells activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding EOS and LEF1, or GATA1 and SATB1. The cells were then sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.
2012-08-23 | E-GEOD-40277 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE40238: Genome-wide maps of FoxP3 binding in transduced CD4+ T cells GSE40273: Gene expression profiling in Treg cells deficient or mutant in candidate FoxP3 cofactors GSE40274: Gene profiling data of CD4+ T cells transduced with FOXP3 and candidate cofactors GSE40276: Gene profiling data of CD4+ T cells transduced with FOXP3 and GATA1, then sorted into different fractions, based on the expression of Thy1.1 (FOXP3) GSE40277: Gene profiling data of CD4+ T cells doubly transduced with EOS+LEF1 or GATA1+SATB1 Refer to individual Series
2012-08-23 | E-GEOD-40278 | biostudies-arrayexpress
Project description:At sites of inflammation, certain Foxp3+ Tregs have the ability to alter their phenotype and become pro-inflammatory helper/effector cells, without losing Foxp3 expression. We show that this functional reprogramming is controlled by the transcription factor Eos (Ikzf4), an obligate co-repressor for Foxp3. The ability to reprogram was restricted to a specific subset of Foxp3+ Tregs, arising as early as the thymus and identifiable by short half-life of Eos at rest, characteristic cell-surface markers (CD38+CD69+CD103NEG) and a distinct pattern of DNA methylation. Mice made selectively deficient in this subset of Eos-labile Tregs became markedly impaired in their ability to cross-present new antigens and prime CD8+ T cells. Downregulation of Eos and consequent Treg reprogramming was prevented by the immunoregulatory enzyme IDO, via activation of the aryl hydrocarbon receptor (AhR). Thus, the Foxp3+ lineage contains a committed subset of Tregs that are constitutively primed for conversion into biologically important helper cells. Cells from thymus or spleen were incubated for 1 hr with cycloheximide (CHX), then CD4+GFP+ Tregs were FACS-sorted into Eos-labile (CD38+CD103NEG) and Eos-stable (CD103+CD38NEG) subsets. Control CD4+GFPNEG (non Treg) cells were sorted from spleen. Genome-wide differential methylation analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS). The genomic DNA from each sample was digested with the methylation-insensitive restriction enzyme MspI (restriction site, CCGG) and ligated to Illumina sequencing adaptors containing methylated cytosine residues. The ligated MspI fragments were size-selected, treated with sodium bisulfite, and amplified by PCR. The PCR products were purified and sequenced using Illumina HiSeq 2000 sequencer with a read length of 100bp.
2013-02-20 | E-GEOD-44380 | biostudies-arrayexpress
Project description:Gene expression profile of FoxP3+ CD4+ follicular regulatory T cells
| PRJNA394986 | ENA
Project description:The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. We used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to assess how cofactors affect the genome-wide localization of FoxP3. Chromatin was prepared from primary CD4+ Tconv cells transfected with FLAG-FoxP3 alone or together with GATA1, immunoprecipitated with anti-FLAG, and the bound DNA determined by Illumina deep sequencing. Immunoprecipitation with anti-PolII, or whole cell extract, provided genome-wide controls for transcriptional start sites (TSSd) or for sequencing non-homogeneity, respectively.
2012-08-23 | E-GEOD-40238 | biostudies-arrayexpress