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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse Th1 and Th17 T helper cells

ABSTRACT: This is to compare the gene expression profile of Th1 and Th17 cells. Experiment Overall Design: Two replicates (rep1, rep2) in two groups (Th1, Th17).

ORGANISM(S): Mus musculus

SUBMITTER: Dongquan Chen

PROVIDER: E-GEOD-14026 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Late developmental plasticity in the T helper 17 lineage.

Lee Yun Kyung YK Turner Henrietta H Maynard Craig L CL Oliver James R JR Chen Dongquan D Elson Charles O CO Weaver Casey T CT

Immunity 20090101 1

Development of T helper (Th) 17 cells requires transforming growth factor (TGF)-beta and interleukin (IL)-6 and is independent of the Th1 pathway. Although T cells that produce interferon (IFN)-gamma are a recognized feature of Th17 cell responses, mice deficient for STAT4 and T-bet-two prototypical Th1 transcription factors-are protected from autoimmunity associated with Th17 pathogenesis. To examine the fate and pathogenic potential of Th17 cells and origin of IFN-gamma-producing T cells that ...[more]

PMID: 19119024

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Methylome of CD4+ T cell subsets

Project description:We compared the methylated and non-methylated regions in the genome of ex vivo-isolated naive CD4+ T cells, Th1 cells, Th17 cells and regulatory T cells by methyl-CpG binding domain protein sequencing (MBD-seq). Naive T cells and Th1 cells share more methylated regions than naive T cells and Th17 cells or Th1 and Th17 cells. However, analysis of the non-methylated regions revealed the highest similarity between Th1 and Th17 cells. Another aim was the analysis of the Th17 lineage on the basis of the methylome. We searched for regions absent in the methylome of Th17 but present in naive T cells, Th1 cells and regulatory T cells. Here, we identified differential methylation in the loci of Il17a, Chn2, Dpp4 and Dclk1. CD4+ T effector cells were prepared ex vivo, stimulated with PMA/Ionomycin, subjected to a comercially available cytokine secretion kit (IL-17A and IFNg), stained by adding fluorescence-labeled antibodies against CD3, CD4 and CD45RB and sorted by flow cytometry. We sorted naive CD4+ T cells (CD3+CD4+CD45RB_high), Th1 cells (CD3+CD4+CD45RB_low_IFNg+IL17A-), Th17 cells (CD3+CD4+CD45RB_low_IFNg-IL17A+) and regulatory T cells (CD3+CD4+CD25++).

2013-12-31 | E-GEOD-45911 | biostudies-arrayexpress

Effects of Th1- and Th17-derived factors on microglia.

Project description:There is evidence that microglia interact with infiltrating Th1 and Th17 cells and this interaction results in mutual activation. However, the potential of a distinct cytokine milieu generated by these effector T cell subsets to activate microglia is poorly understood. In this study, we tested the ability of factors secreted by Th1 and Th17 cells to induce microglial activation. Interestingly, we found that only Th1-associated factors had the potential to activate microglia while the Th17-associated factors as well as direct contact of Th17 cells with microglia only had a minimal effect. Further Th1-derived factors triggered a proinflammatory M1-type gene expression profile in microglia Microglia harvested from mixed glial cultures were treated with supernatants from Th1- or Th17 cultures. Microglia cultured in medium was used as controls. At 16h post treatment RNA was isolated from the microglia and probed on AgilentÂ´s murine 4x44k microarrays. RNA isolated from four independent experiments were used for the gene expression profiling. Microglia, Th1, Th17

2013-12-31 | E-GEOD-45384 | biostudies-arrayexpress

Gene expression data from polarized T helper cells isolated from mice with opticospinal (OSE) experimental autoimmune encephalomyelitis (EAE)

Project description:T cells from the spleen of a mixed-gender pool of four double-transgenic 2D2 (TCRMOG) x IgHMOG mice (OSE) mice, which spontaneously develop experimental autoimmune encephalomyelitis (EAE), were used to derive TH1- and TH17-polarized cells, as described in https://doi.org/10.1371/journal.pone.0015531. Here, expression was compared, first, between TH1 and naïve TH0 and, second, between TH17 and naïve TH0 cells.

2020-08-21 | E-MTAB-9133 | biostudies-arrayexpress

Compare gene expression profiles of TCR transgenic CD4+ T helper type 1 (Th1) vs. type 17 (Th17) cells optimally stimulated by antigen and differentiated under Th1 or Th17 conditions.

Project description:The comparison of Th1 vs. Th17 cell expression profile has been plagued by 1) rarely use of physiologically relevant antigen-driven T helper cell differentiation; and 2) cell lineage tracking system to enrich highly pure Th subsets. We began our attempt to produce large numbers of antigen-specific T helper subsets for expression profiling, when Foxp3GFP knockin mice were first made by our laboratory in 2005. We crossed this line with syngeneic TEa TCR transgenic mice in C57BL/6 background, and use FACS to sort optimally stimulated, highly pure GFP(Foxp3)-negative populations for Th1 vs. Th17 expression profile comparison.

2019-03-15 | E-MTAB-7661 | biostudies-arrayexpress

Analysis of gene expression in different T cell clones

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2008-05-30 | E-GEOD-11553 | biostudies-arrayexpress

Expression and functions of long noncoding RNAs during human T helper cell differentiation

Project description:To improve our understanding of lncRNA expression in T cells, we used whole genome sequencing (RNA-seq) to identify lncRNAs expressed in human T cells and those selectively expressed in T cells differentiated under TH1, TH2, or TH17 polarizing conditions. The majority of these lineage-specific lncRNAs are co-expressed with lineage-specific protein-coding genes. These lncRNAs are predominantly intragenic with co-expressed protein-coding genes and are transcribed in sense and antisense orientations with approximately equal frequencies. Further, genes encoding TH lineage specific mRNAs are not randomly distributed across the genome but are highly enriched in the genome in genomic regions also containing genes encoding TH lineage-specific lncRNAs. Our analyses also identify a cluster of antisense lncRNAs transcribed from the RAD50 locus that are selectively expressed under TH2 polarizing conditions and co-expressed with IL4, IL5 and IL13 genes. Depletion of these lncRNAs via selective siRNA treatment demonstrates the critical requirement of these lncRNAs for expression of the TH2 cytokines, IL-4, IL-5 and IL-13. Collectively, our analyses identify new lncRNAs expressed in a TH lineage specific manner and identify a critical role for a cluster of lncRNAs for expression of genes encoding TH2 cytokines. Human peripheral blood mononuclear cells (PBMC) were cultured under TH1, TH2, and TH17 polarizing conditions. TH1, TH2, and TH17 primary and effector cultures were isolated and poly(A)+ and total RNA sequencing performed.

2015-04-23 | E-GEOD-66261 | biostudies-arrayexpress

Ezh2 chip-seq of Th1 and Th2 cells during the first 48 hours of cell differentiation.

Project description:CD4 T helper cells can differentiate to several types of cells like Th1, Th2, Th17 and Treg. This process is directed by cytokines and activation of T cells by specific antigens. This process has its own plasticity and it is directed by epigenetic changes allowing cells to develop and differentiate. In this experiment, we wanted to explore the binding pattern of EZH2 in the first 24 and 48 hours of Th cells activation and differentiation.

2021-08-28 | E-MTAB-9594 | biostudies-arrayexpress

Project Title: Proteome analysis of CD4+ T cell subsets

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2023-01-04 | PXD036065 | JPOST Repository

Chip-seq of EZH2 and VAV1 in 24hr differentiated Th1 and Th2 cells with or without EZH2 or Actin polymerization inhibitors

Project description:CD4 T helper cells can differentiate to several types of cells like Th1, Th2, Th17 and Treg. This process is directed by cytokines and activation of T cells by specific antigens. This process has its own plasticity and it is directed by epigenetic changes allowing cells to develop and differentiate. In this experiment, we wanted to explore the binding pattern of EZH2 in the first 24 hours of Th cells activation and differentiation side by side with VAV1 binding pattern to understand the importance of actin polymerization factors in this process.

2021-08-28 | E-MTAB-9524 | biostudies-arrayexpress

Transcriptional profiles of CCR7lo effector memory human T cell subsets

Project description:The aim of this study was to identify differentially-expressed genes in CCR4hi/CXCR3- and CCR4lo CXCR3+ CCR6+ human Th17 cell subsets Human CD45RO+ memory T cells isolated from the peripheral blood of healthy adult donors were sorted into 4 predominant CCR7lo CD25- effector memory subsets: (1) Th1 - CCR6- CCR4lo CXCR3+; (2) Th2 - CCR6- CCR4hi CXCR3+; (3) Th17 - CCR6+ CCR4hi CXCR3-; (4) Th17.1 - CCR6+ CCR4lo CXCR3-. Sorted cells were cultured in media and activated via anti-CD3/anti-CD28 beads for 36 hours. All subsets were then harvested and used for RNA extraction and microarray experiments. Th1 vs Th2; Th1 vs Th17; Th1 vs Th17.1; Th2 vs Th17; Th2 vs Th17.1; Th17 vs Th17.1

2013-12-17 | E-GEOD-49703 | biostudies-arrayexpress

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