Similar studies for GEO DataSets (Select 200076030) - GEO DataSets

Select item 2000760301.

Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses (RNA-Seq)

(Submitter supplied) Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
3 Samples

Download data: TXT

Series

Accession:: GSE76030

ID:: 200076030

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000855602.

Genome structure and organization in mouse CD8 T cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL17021
7 Samples

Download data: TXT, WIG

Series

Accession:: GSE85560

ID:: 200085560

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Select item 2000855153.

Genome structure and organization in mouse CD8 T cells [Hi-C-seq]

(Submitter supplied) Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. more...

Organism:: Mus musculus

Type:: Other

Platform:: GPL17021
3 Samples

Download data: TXT

Series

Accession:: GSE85515

ID:: 200085515

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Select item 2000855134.

Genome structure and organization in mouse CD8 T cells [RNA-seq]

(Submitter supplied) Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
4 Samples

Download data: WIG

Series

Accession:: GSE85513

ID:: 200085513

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Select item 2000760315.

Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
18 Samples

Download data: TXT, WIG

Series

Accession:: GSE76031

ID:: 200076031

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Select item 2000760296.

Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses (ChIP-Seq)

(Submitter supplied) Our experiments aimed to investigate the landscape of enhancers and super-enhancers in naïve, effector and memory CD8+ T cells. Here we mapped four histone modification marks and gene expression in naive, effector, and memory cells after viral infection. Our results suggest that the chromatin environment at regulatory DNA sequences in TCM is more permissive than in TN and TE. We further predicted the enhancers and their targets, and constructed transcriptional regulatory networks (TRNs) in three T cell stages. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
15 Samples

Download data: WIG

Series

Accession:: GSE76029

ID:: 200076029

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Select item 2001504427.

P14 CD8 T cells during acute LCMV infection

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19057
27 Samples

Download data: BW

Series

Accession:: GSE150442

ID:: 200150442

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Select item 2001423448.

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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL19057
12 Samples

Download data: BW

Series

Accession:: GSE142344

ID:: 200142344

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Select item 2001301309.

Characterization of CD8 T cells during acute LCMV infection using scRNA-seq

(Submitter supplied) During a viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off each individual T cell on a unique differentiation trajectory. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection—death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the dynamic transcriptional changes during effector and memory CD8 T cell differentiation at the single cell level.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
3 Samples

Download data: MTX, TSV

Series

Accession:: GSE130130

ID:: 200130130

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Select item 20006805610.

Transcriptional profiling of antigen-specific CD8 T cells from wildtype and mutant mice.

(Submitter supplied) To understand CD8 effector T cell differentiation in more detial we have used transcriptional profiling of antigen-specific CD8 T cells deficient in Blimp1, IL-2ra, or both, or Tbet. We reveal a common program of effector differentiation regulated by cytokine signaling and the combined activities of Blimp1 and T-bet, indicating remarkable redundancy and specificity in the control of genes involved in the differentiation of effector T cells.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9185
16 Samples

Download data: TXT

Series

Accession:: GSE68056

ID:: 200068056

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Select item 20008898711.

Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection

(Submitter supplied) In response to acute infection, naive CD8+ T cells expand, differentiate into effector cells and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8+ T cells acquire an “exhausted” phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8+ T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq. more...

Organism:: Mus musculus

Type:: Other; Expression profiling by high throughput sequencing

Platform:: GPL17021
44 Samples

Download data: TSV

Series

Accession:: GSE88987

ID:: 200088987

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Select item 20014215112.

Chromatin states and transcriptome of CD8+ T cells over the course of differentiation

(Submitter supplied) The goal of this study is to analyze the contribution of transposable elements (TEs) tocis-regulation in CD8+ T cells. Using a combination of NGS techniques we show that specific subfamilies of TEs are enriched, and distributed in a lineage-specific fashion in core and boundary domains of CD8+T cell enhancers.This study represents the first detailed analysis of the topology and the enhancer domain-associated putative functions of distinct TE types.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
23 Samples

Download data: BW, WIG

Series

Accession:: GSE142151

ID:: 200142151

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Select item 20004463813.

Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function

(Submitter supplied) In response to acute infection CD8 T cells differentiate into effector cells capable of clearing the antigen. While the transcriptional and functional changes have previously been studied little is known of the epigenetic modifications that accompany this differentiation process. To gain insights into CD8 T cell effector differentiation and the role of epigenetics, we mapped DNA methylation by MeDIP-seq in naive CD8 T cells and day 8 effector CD8 T cells that are induced following an acute infection. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13112
3 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE44638

ID:: 200044638

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Select item 20008315914.

Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Methylation profiling by array; Methylation profiling by genome tiling array; Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL13534 GPL10558 GPL15456
31 Samples

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Series

Accession:: GSE83159

ID:: 200083159

Select item 20008315815.

Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_12_Gene_Expression]

(Submitter supplied) Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
4 Samples

Download data: TXT

Series

Accession:: GSE83158

ID:: 200083158

Select item 20008315716.

Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_07_Gene_Expression]

(Submitter supplied) Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
6 Samples

Download data: TXT

Series

Accession:: GSE83157

ID:: 200083157

Select item 20008315617.

Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_05_Methylation]

(Submitter supplied) Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array; Methylation profiling by genome tiling array

Platform:: GPL13534
6 Samples

Download data: TXT

Series

Accession:: GSE83156

ID:: 200083156

Select item 20008315518.

Epigenetic regulation of the transcriptional program in memory and terminally differentiated CD8+ T cells [HCAFIS_03_ChIPseq]

(Submitter supplied) Epigenetic mechanisms play a critical role during differentiation of T cells by contributing to the formation of stable and heritable transcriptional patterns. To further study the mechanisms of memory maintenance in CD8+ T cells, we performed genome-wide analysis of DNA methylation, histone marking (H3K9Ac and H3K9me3) and gene expression profiles in naive, effector memory (EM) and terminally differentiated memory (TEMRA) cells. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL15456
15 Samples

Download data: TXT

Series

Accession:: GSE83155

ID:: 200083155

PubMed Similar studies SRA Run Selector

Select item 20007164319.

Translational profiling of in vivo virus-specific CD8 T cells

(Submitter supplied) Translation is a critical cellular process to synthesize proteins from their transcripts. However, translational regulation in antigen-specific T cells in vivo has not been well defined. To address this question, we performed microarray analyses of both total and polysome-associated mRNAs in antigen specific CD8 T cells after acute viral infection.