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Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls

ABSTRACT: Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls

PROVIDER: PRJNA383107 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5453090.fastq.gz	Fastqsanger.gz
	SRR5453100.fastq.gz	Fastqsanger.gz
	SRR5453110.fastq.gz	Fastqsanger.gz
	SRR5453120.fastq.gz	Fastqsanger.gz
	SRR5453130.fastq.gz	Fastqsanger.gz

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Project description:Histone methylations play a major role in regulating the chromatin state and gene expression, yet little is known about their involvement in differential gene expression and function of memory CD8 T cells. Here, we report a genome-wide analysis of two histone H3 methylations (H3K4me3 and H3K27me3) and gene expression in naïve, central (TCM) and effector (TEM) memory CD8 T cells. Analysis of 16,314 annotated genes in CD8 T cell subsets revealed that gene expression were positively correlated with the levels of H3K4me3 and negatively correlated with the levels of H3K27me3 in these gene loci. The correlation between differential H3K4me3 orH3K27me3 levels with gene expressions in memory CD8 T cells displayed four distinct modes: repressive, active, poised, and bivalent, reflecting their complex regulation and different function of these genes. Furthermore, accessible chromatin states of different gene loci were preferentially influenced by different histone modifications as demonstrated here high levels of H3K9ac found in active gene loci without high levels of H3K4me3. These findings reveal a histone methylation based complex regulation of differential gene expression in memory CD8 T cells. Thus, change of chromatin structure mediated by histone methylation may serve a fundamental basis for the rapid transcriptional response of memory CD8 T cells. Keywords: Histone methylations, chromatin state, CD8 memory T cells Enriched naïve and memory CD8 T cells were purified into CD8+CD45RA+CD62L+ naïve T cells, CD8+CD45RA-CD62L+ central memory T cells (TCM), and CD8+CD45RA-CD62L- effector memory T cells (TEM) by a cell sorter (MoFlo; Dako Cytomation, Carpentaria, CA). Triplicates of each cell type were either used right away or incubated with anti-CD3 and anti-CD28 Ab (anti-CD3/CD28) coupled magnetic beads (Invitrogen) at the cell:bead ratio of 1:1 for 16 hours in RPMI-1640 with 10% Fetal bovine serum and penicillin (10 U/ml)/streptomycin (10 ug/ml) (Invitrogen). The freshly isolated and 16 hr stimulated cells from several donors as a pool were used for gene expression microarray analysis. All sample data was normalized to a standard control RNA labeled and hybed along with each sample and all data from the 3 replicates was averaged.

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Transcriptomic profile of circulating naïve, TCM, TEM and TEMRA T cells in donors from Sri Lanka previously exposed to dengue virus and healthy controls

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