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Gene expression in thymic CD4 T cells: effects of Foxp3

ABSTRACT: This data set is comprised of all thymic T cell subsets presented in this manuscript. These include T-N, T-25, T-FN and T-R thymocytes. Keywords: cell type comparison, development

ORGANISM(S): Mus musculus

PROVIDER: GSE7770 | GEO | 2007/05/18

SECONDARY ACCESSION(S): PRJNA105489

REPOSITORIES: GEO

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Transcription profiling of human thymic T cell subsets T-N, T-25, T-FN and T-R thymocytes

Project description:This data set is comprised of all thymic T cell subsets presented in this manuscript. These include T-N, T-25, T-FN and T-R thymocytes. Experiment Overall Design: Detailed methods are presented in the manuscript and in the attached Supplementary Information. All RNA samples were derived from cells immediately after isolation from mice. Note that these samples were amplified and labeled with Affymetrix and Enzo reagents, while peripheral T cell samples were amplified and labeled with Ambion reagents.

2008-06-15 | E-GEOD-7770 | biostudies-arrayexpress

Gene expression in peripheral cells: effects of Foxp3 and PDE3B

2007-05-18 | GSE7280 | GEO

Transcription profiling of mouse peripheral T cells subsets: T-N, T-25, T-FN and T-R cells; T-25, T-FN and T-R cells after treatment with IL-2; and T-R cells transduced with empty, PDE3B-expressing or PDE3B(H801A)-expressing retroviral vectors

Project description:This data set is comprised of all peripheral (pooled lymph nodes and spleen) T cell subsets presented in this manuscript. These include T-N, T-25, T-FN and T-R cells; T-25, T-FN and T-R cells from mice treated with IL-2; and T-R cells transduced with empty, PDE3B-expressing or PDE3B(H801A)-expressing retroviral vectors (after transfer into recipient mice). Experiment Overall Design: Detailed methods are presented in the manuscript and in the attached Supplementary Information. All RNA samples were derived from cells immediately after isolation from mice. Although this data set is comprised of 2 separate experiments (cells isolated from normal mice or IL-2 treated mice and cells transduced with retroviral vectors and passaged through recipient mice), the 10 expression arrays were normalized together to allow for cross comparison.

2008-06-15 | E-GEOD-7280 | biostudies-arrayexpress

Transcription profiling time series of thymocytes from HNT-TCR transgenic mice injected with HA peptide to induce thymic negative selection

Project description:During T cell development in the thymus, negative selection eliminates autoreactive and potentially harmful T cells, leading to central tolerance. This process, involves specific apoptosis programs thought to be governed by the transcription factor Nur77. To analyze the genetic pathways involved in thymic negative selection and to point to new genes involved in thymic selection, we performed a high throughput temporal expression profiling of thymocytes from HNT-TCR transgenic mice undergoing specific peptide-mediated thymic negative selection, using oligonucleotide microarrays. We used HNT-TCR transgenic mice that are on a B10D2 background and express a transgenic TCR (V beta 8), specific for the HA peptide (HNTNGVTAACSHE) presented by MHC class II I-A^d. In this model of thymic negative selection, a single injection of the specific HA peptide induces massive and synchronized deletion of thymocytes. In this study, we analyzed the dynamically regulated genes over a 24 hours period, with a focus on the early time points of 3 and 6 hours after peptide injection.

2011-06-20 | E-TABM-550 | biostudies-arrayexpress

Thymic epithelial cells induce formation of mesenchymal network structure after abrogation of thymic crosstalk

Project description:In the earliest step of thymic organogenesis, mesenchymal cells support the growth of thymic epithelial cells (TECs). It is established that TECs and thymocytes influence each other for their growth/differentiation, a process called thymic crosstalk. However, little is known about the influence of developing thymocytes or TECs on mesenchymal cells. Here, we show that during normal thymus development fibroblast ingrowth occurs towards hypoxic areas. Similar overgrowth of mesenchymal cells is seen in a fetal thymic organ culture system under low oxygen conditions. However, when thymocytes were depleted by deoxyguanosine treatment, mesenchymal cells were also induced, precluding the direct effect of hypoxia. In the fetal thymus of hCD3εTg mice, which lack T lineage cells, an overgrowth of mesenchymal cells can be seen at a very early stage of thymic organogenesis. The growth of the mesenchymal cells is due to extensive proliferation and not mere enrichment. With RNA sequencing analysis comparing hCD3εTg with wild type TECs, we identified candidate factors that could be involved in mesenchymal network formation.

2017-08-19 | GSE60520 | GEO

Silencing of C2TA reveals the autonomous role of medullary thymic epithelial cells in central CD4 T cell tolerance

Project description:[original title] Tissue-specific silencing of C2TA reveals the autonomous role of medullary thymic epithelial cells in central CD4 T cell tolerance. Medullary thymic epithelial cells (mTECs) serve an essential function in central tolerance through expressing peripheral tissue-antigens. Because these antigens may be transferred to and presented by Dendritic Cells, it is unclear whether, besides being an ‘antigen reservoir’, mTECs also fulfill a critical antigen presenting cellfunction. We found that reducing MHC class II-levels on mTECs through transgenic expression of a C2TA-specific ‘designer miRNA’ resulted in an enlarged polyclonal CD4 single-positive compartment. Less CD4+ thymocytes specific for model-antigens expressed in mTECs were deleted, whereas more antigen-specific Foxp3+ regulatory T cells (Treg) emerged. Our data suggest a substantial autonomous contribution of mTECs to both dominant and recessive mechanisms of CD4 T cell tolerance and support an avidity model of Treg development versus deletion.

2010-02-11 | GSE20276 | GEO

Ikaros mutant thymic tumors

Project description:The experiment was to compare leukemic T cells from thymic lymphomas from homozygote mice for the IkL/L hypomorphic mutation and non-transformed thymocytes, either of WT or IkL/L genotype. The aim was to identify a gene expression signature specific to the IkL/L tumors. Keywords = thymic lymphoma Ikaros Keywords: other

2005-05-06 | GSE2501 | GEO

Transcription profiling of mouse fetal thymic organ culture BDC2.5 CD4+CD8+ thymocytes from B6g7 or NOD strain backgrounds following addition of the BDC mimotope peptide

Project description:Fetal thymic organ culture (FTOC) DC2.5 CD4+CD8+ thymocytes from B6g7 or NOD background. 0 or 16 hour after addition of the BDC mimitope

2007-12-04 | E-GEOD-2128 | biostudies-arrayexpress

RNAseq analysis of mature thymic NKT cells and immature thymic DN1eP cells

Project description:We report the identification of immature thymic CD4(-),CD8(-) double-negative (DN)1e cells with the NKT cell lineage potential. We also analyzed the gene expression profiles of DN1e thymocytes compared with those of mature thymic NKT cell developmental stages termed NKT stage-1, 2, and -3, which are characterized by differential expression levels of NK1.1 and CD44 antigens in C57BL/6 mouse strain. Next generation sequencing of total transcriptomes using total RNA isolated from FACS sorted ex vivo thymic DN1eP (Lin-/CD44+/CD25-/CD24low/CD5+/CD27+/Ly108-/CXCR3+) fraction, and mature thymic alphaGalCer-loaded CD1d dimer+TCRbeta+ NKT cell developmental stage-1 (CD44-/NK1.1-), stage-2 (CD44+/NK1.1-), and stage-3 (CD44+/NK1.1+) cells.

2015-12-31 | E-GEOD-53150 | biostudies-arrayexpress

Transcriptome analysis of murine thymocytes reveals age-associated changes in thymic gene expression

Project description:The decline in adaptive immunity, naïve T-cell output and a contraction in the peripheral T cell receptor (TCR) repertoire with age are largely attributable to thymic involution and the loss of critical cytokines and hormones within the thymic microenvironment. To assess the molecular changes associated with this loss of thymic function, we used cDNA microarray analyses to examine the transcriptomes of thymocytes from mice of various ages ranging from very young (1 month) to very old (24 months). Genes associated with various biological and molecular processes including oxidative phosphorylation, T- and B- cell receptor signaling and antigen presentation were observed to significantly change with thymocyte age. These include several immunoglobulin chains, chemokine and ribosomal proteins, annexin A2, vav 1 and several S100 signaling proteins. The increased expression of immunoglobulin genes in aged thymocytes could be attributed to the thymic B cells which were found to be actively producing IgG and IgM antibodies. Upon further examination, we found that purified thymic T cells derived from aged but not young thymi also exhibited IgM on their cell surface suggesting the possible presence of auto-antibodies on the surface thymocytes with advancing age. These studies provide valuable insight into the cellular and molecular mechanisms associated with thymic aging. Keywords: Thymocytes, thymic involution, aging, time course

2009-05-05 | GSE15945 | GEO

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