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RNA-seq of ATF7ip-deficient T cells

ABSTRACT: RNA-seq of ATF7ip-deficient T cells

PROVIDER: PRJNA543904 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9097940.fastq.gz	Fastqsanger.gz
	SRR9097950.fastq.gz	Fastqsanger.gz
	SRR9097960.fastq.gz	Fastqsanger.gz
	SRR9097941.fastq.gz	Fastqsanger.gz
	SRR9097951.fastq.gz	Fastqsanger.gz

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RNA-seq of ATF7ip-deficient T cells

Project description:RNA-seq performed in ATF7ip-deficient T cells reveals a defect in Th17 gene induction secondary to increased IL-2 T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

2019-05-21 | GSE131533 | GEO

H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

Project description:T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

2019-05-21 | GSE131511 | GEO

H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

Project description:H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

| PRJNA543885 | ENA

ATF7ip targets transposable elements for H3K9me3 deposition to modify CD8+ T cell effector and memory responses

Project description:Method: To study the effector response of Atf7ip, a) we infected Atf7ip+/fl and Atf7ipfl/fl mice with lcmv . RNAseq was performed using CD8 T cells isolated from Lymph node and Spleen of Het and KO mice. RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. The RNA-Seq was performed by UCSF core using Illumina Platform. RNAseq was also carried out using naive CD8 T cells isolated from Atf7ip+/fl and Atf7ipfl/fl mice along with Atf7ip+/fl and Atf7ipfl/fl CD8 T cells stimulated for 72 hrs. This set of samples were sequenced using commercial facility from Genewiz, USA. Results: Our transcriptome analysis (RNA-seq) identified, Il7r, Runx3 etc. to be upregulated in the Atf7ipfl/fl CD8 T cells as compared to the Atf7ip+/fl CD8 T cells.

2021-12-21 | GSE190417 | GEO

HIRA loss transforms FH deficient cells [RNA-Seq]

Project description:HIRA loss transforms FH deficient cells [RNA-Seq]

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RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

Project description:RNA-seq of Tgfbr2-deficient thymic iNKT1 cells

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RNA-Seq and ChIP-Seq in SIX1 deficient Rhabdomyosarcoma cells

Project description:RNA-Seq and ChIP-Seq in SIX1 deficient Rhabdomyosarcoma cells

| PRJNA723882 | ENA

small RNA-Seq of miR-181 deficient Treg cells

Project description:small RNA-Seq of miR-181 deficient Treg cells

| PRJNA512620 | ENA

RNA-seq analysis with MFN2-deficient human iPS cells

Project description:RNA-seq analysis with MFN2-deficient human iPS cells

| PRJNA939711 | ENA

Assessing the impact of loss of ATF7IP and SETDB1 on the transcriptome

Project description:By comparing HeLa cells lacking ATF7IP or SETDB1 generated through CRISPR/Cas9-mediated gene disruption to wild-type HeLa cells, the goal of the experiment was to determine the effect of loss of the SETDB1•ATF7IP complex on the transcriptome.

2016-10-11 | GSE86813 | GEO

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