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Epigenetic profiling of primary human peripheral blood NK cell populations

ABSTRACT: Epigenetic profiling of primary human peripheral blood NK cell populations

PROVIDER: PRJNA525105 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8650120.fastq.gz	Fastqsanger.gz
	SRR8650130.fastq.gz	Fastqsanger.gz
	SRR8650121.fastq.gz	Fastqsanger.gz
	SRR8650131.fastq.gz	Fastqsanger.gz
	SRR8650122.fastq.gz	Fastqsanger.gz

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Epigenetic profiling of primary human peripheral blood NK cell populations

Project description:Human peripheral blood NK cell popiulations were seperated on the basis of CD56 expression with flowcytometry. Sorted CD56-bright (CD56Br) and CD56-dim (CD56Dim) NK cells were subjected to H3K4Me2 ChIPmentation to obtain epigenome profiles for downstream analyses.

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Expression data of Human Decidual NK cells, Peripheral blood, CD56Bright NK cells and CD56Dim NK cells on HGU133A arrays

Project description:Fragmented RNA cocktails from FACS sorted Human decidual NK cell, and peripheral blood CD56Bright and CD56Dim NK cells, previously hybridization to HGU95AV2 chips (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-1), were stored long term at -80C, thawed and hybridized to HG-U133A arrays. Transcriptome analysis of Human decidual NK cells and NK cells from peripheral blood using Affymetrix UGU133A arrays.

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Expression data of Human Decidual NK cells, Peripheral blood, CD56Bright NK cells and CD56Dim NK cells on HGU133B arrays

Project description:Fragmented RNA cocktails from FACS sorted Human decidual NK cell, and peripheral blood CD56Bright and CD56Dim NK cells, previously hybridization to HGU95AV2 chips (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-1), were stored long term at -80C, thawed and hybridized to HG-U133B arrays. Transcriptome analysis of Human decidual NK cells and NK cells from peripheral blood using Affymetrix UGU133B arrays.

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Diversity of peripheral blood human NK cells identified by single cell RNA sequencing

Project description:Human Natural Killer (NK) cells in peripheral blood perform many functions but classification of specific subsets has been a long-standing problem. Here, we report single-cell RNA sequencing of NK cells from healthy CMV-negative donors, comparing gene expression in unstimulated and IL-2 activated cells. Unsupervised clustering identified seven NK cell subsets. Three resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which were CD56neg; a population exhibiting an in-vivo cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2, and finally, a small population, with low ribosomal expression, down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Human cytomegalovirus positive donors also included a higher frequency of adaptive NK cells. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analysing NK cell responses in health and disease.

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Project description:Human Natural Killer (NK) cells in peripheral blood perform many functions and classification of specific subsets has been a long-standing goal. Here, we report single cell RNA-sequencing of NK cells, comparing gene expression in unstimulated and IL-2 activated cells, from healthy CMV-negative donors. Three NK cell subsets resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which were CD56neg, a population exhibiting a cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2, and finally, a small population, with low ribosomal expression, down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Analysis of CMV-positive donors established that CMV altered the proportion of NK cells in each subset, especially an increase in adaptive NK cells, as well as gene regulation within each subset. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analysing NK cell responses in health and disease.

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RUNX2-specific ChIP of human peripheral blood NK cells

Project description:RUNX2-specific ChIP of human peripheral blood NK cells

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