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ATAC-seq of MIG, MIG-E47, or MIG-ID2 transduced CD8 T cells in vitro

ABSTRACT: We performed RNA-seq and ATAC-seq on in vitro activated P14 CD8 T cells transduced with MIG (empty), MIG-E47, or MIG-ID2.

ORGANISM(S): Mus musculus

PROVIDER: GSE142342 | GEO | 2021/04/02

REPOSITORIES: GEO

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RNA-seq of MIG, MIG-E47, or MIG-ID2 transduced CD8 T cells in vitro

Project description:We performed RNA-seq and ATAC-seq on in vitro activated P14 CD8 T cells transduced with MIG (empty), MIG-E47, or MIG-ID2.

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MIG, MIG-E47, or MIG-ID2 transduced CD8 T cells in vitro

Project description:This SuperSeries is composed of the SubSeries listed below.

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Transcriptome of SATB1 transduced Hut78 cells

Project description:Hut78 cell line was used as Sezary syndrome cell model. Comparative transcriptome profiles of SATB1 transduced Hut78 cells (Hut78-SATB1) relative to empty MIG vector transduced control Hut78 cells (Hut78-MIG) were analyzed. The primary goal is to establish a list of genes with differential expression between SATB1 transduced Hut78 cells and control Hut78 cells to identify the gene expression regulation effect of SATB1 expression in Sezary cells.

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Identification of E47 targets

Project description:In maturing T-lineage cells, the helix-loop-helix protein E47 has been shown to enforce a critical proliferation and developmental checkpoint commonly referred to as Î² selection. To examine how E47 regulates cellular expansion and developmental progression, we have used an E2A deficient lymphoma cell line and DNA microarray analysis to identify immediate E47 target genes. Hierarchical cluster analysis of gene expression patterns revealed that E47 coordinately regulates the expression of genes involved in cell survival, cell growth, lipid metabolism, stress response and lymphoid maturation. These include Cdk6, CD25, Tox, Gadd45a, Gadd45b, Gfi1, Gfi1b, Socs1, Socs3, Id2, Eto2 and Xbp1. We propose a regulatory network linking JAK/STAT mediated signaling, E47 and SOCS proteins in a common pathway. Finally, we suggest that the aberrant activation of Cdk6 in E47 deficient T-lineage cells contributes to the development of lymphoid malignancy. We used the 1F9 cell line, originally isolated from E2A deficient thymomas. To identify E47 target genes, 1F9 cells were transduced with a retrovirus carrying an E47/estrogen receptor (E47ER) hybrid protein. Control cells were transduced with virus carrying the bHLH region but lacking the N-terminal transactivation domain. Both retroviral constructs also directed the expression of human CD25 (hCD25) to allow rapid isolation of transduced cells. One day post-infection, cells were incubated with 4-hydroxytamoxifen (4-OHT) for a period of six hours, to activate the E47ER fusion protein. hCD25 positive cells were purified using magnetic beads, RNA was isolated and used to generate probes for hybridization to murine oligonucleotide microarrays.

2010-07-01 | E-GEOD-4784 | biostudies-arrayexpress

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Identification of E47 targets

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Expression data of in vitro generated regulatory T cells overexpressing E47

Project description:E47 represses Foxp3 transcription, albeit indirectly through the activation of unknown negative regulatory of Foxp3 transcription. To identify target genes of E47 in regulatory T cells, we compared gene expression profiles of Treg cells overexpressing E47 compared to control-vector transduced cells.

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