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Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (60K)

ABSTRACT: Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (60K)

PROVIDER: PRJNA445876 | ENA |

REPOSITORIES: ENA

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Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (60K)

Project description:Aging of immune system is characterized by progressive decline of physiological and cellular function of T cells. Recent studies of naïve T cells from young and old mice have identified age-related altered gene expressions but the mechanisms underlying age associated changes of naïve T cells remain poorly understood. Here we compared the transcriptome and chromatin accessibility in mature CD4 and CD8 thymocytes and in naïve CD4 and CD8 T cells of spleen between young (6-8 weeks) and old (79-121 weeks) C57Bl/6 mice. We used Agilent microarray method and identified the age-related altering gene expressions 1) only in mature CD4 and CD8 T cell from thymus, 2) shared by both thymus and spleen naïve T cells, and 3) only in naïve T cells from spleen. The shared changes include increased chemokine and chemokine receptor expressions and decreased cell cycle regulator expression. We further analyzed the chromatin basis of altered gene expression using Assaying Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) between young and old mice. We have identified age-related changes of chromatin accessibility in T cells from thymus and spleen, and some correlated changes between gene expression and chromatin accessibility. Overall, we observedmore age-related alterations of gene expression and chromatin accessibility inthymus than in spleen, suggesting some age-related changes of T cells in thymus did not retain in periphery. Together, our findings have identified tissue specific altered gene expressions and chromatin status in T cells during aging and further study of these altered genes will shed new insights into the mechanisms underlying these age-related changes.

2021-03-19 | GSE112391 | GEO

Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (44K)

2021-03-19 | GSE112390 | GEO

Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery

Project description:Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery

| PRJNA445870 | ENA

Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (44K)

Project description:Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (44K)

| PRJNA445874 | ENA

scATAC-seq of fetal thymus

Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.

2021-11-30 | E-MTAB-9828 | biostudies-arrayexpress

Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery

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

2021-03-19 | GSE112392 | GEO

Project description:The human thymus shows a transient involution along the neonatal period and starts a continuous process of decline between the 1st and 2nd years. The immune alterations associated to thymic aging in humans have been extensively investigated, but the genomic mechanisms underlying this process remain largely unknown. Here we conducted a temporal gene co-expression network analysis in the newborn and infant thymic tissue aiming to identify transcriptional modules associated to age.

2019-12-27 | GSE131191 | GEO

2019-12-27 | GSE131241 | GEO

scRNA-seq of human fetal thymus

2021-11-30 | E-MTAB-9840 | biostudies-arrayexpress

A widespread decrease of chromatin accessibility in age-related macular degeneration

Project description:Age-related macular degeneration (AMD) is a leading cause of blindness in the elderly. The extent to which epigenetic changes regulate the progression of AMD is unclear. Here we profiled chromatin accessibility in the retina and retinal pigmented epithelium (RPE) from AMD patients and controls. Global decreases in chromatin accessibility occur in the RPE in early AMD and in the retina with advanced disease. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs) and reduced AMD. Genes associated with DARs show altered expression in AMD. Cigarette smoke, an established risk factor for AMD, applied to human iPSC-derived RPE cells recapitulates epigenomic changes seen in AMD. In addition to providing a comprehensive profile of chromatin accessibility in human RPE and retina, this study shows that global decreases in chromatin accessibility may play a critical role in AMD progression.

2018-03-05 | GSE99287 | GEO

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