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Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection [RNA-seq]

ABSTRACT: Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection [RNA-seq]

PROVIDER: PRJNA642891 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12112610.fastq.gz	Fastqsanger.gz
	SRR12112611.fastq.gz	Fastqsanger.gz
	SRR12112612.fastq.gz	Fastqsanger.gz
	SRR12112613.fastq.gz	Fastqsanger.gz
	SRR12112614.fastq.gz	Fastqsanger.gz

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Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection

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Project description:Sepsis, sequela of bloodstream infections and dysregulated host responses, is a leading cause of death globally. Neutrophils tightly regulate responses to pathogens to prevent organ damage. Profiling early host epigenetic responses in neutrophils may aid in disease recognition. We performed assay for transposase-accessible chromatin (ATAC)-seq of human neutrophils challenged with six toll-like receptor ligands and two organisms; and RNA-seq after Escherichia coli exposure for 1 and 4 h along with ATAC-seq. ATAC-seq of neutrophils facilitates detection of pathogen DNA. In addition, despite similarities in genomic distribution of differential chromatin changes across challenges, only a fraction overlaps between the challenges. Ligands depict shared signatures, but majority are unique in position, function, and challenge. Epigenomic changes are plastic, only ∼120 are shared by Ecoli challenges over time, resulting in varied differential genes and associated processes. We identify three classes of gene regulation, chromatin access changes in the promoter; changes in the promoter and distal enhancers; and controlling expression through changes solely in distal enhancers. These and transcription factor footprinting reveal timely and challenge specific mechanisms of transcriptional regulation in neutrophils.

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Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection

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Project description:Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection.

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Project description:We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq. In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10. DNase-Seq was carried out in WT and SRC-2-/- mice in liver at CT10 using two doses of DNaseI.

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