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Mus musculus

ABSTRACT: Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps [ATAC-seq]

PROVIDER: PRJNA352061 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4785160_1.fastq.gz	Fastqsanger.gz
	SRR4785160_2.fastq.gz	Fastqsanger.gz
	SRR4785170_1.fastq.gz	Fastqsanger.gz
	SRR4785170_2.fastq.gz	Fastqsanger.gz
	SRR4785180_1.fastq.gz	Fastqsanger.gz

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Mus musculus

Project description:Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps [ATAC-seq]

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Project description:Integrative analysis of single-cell ATAC-seq and RNA-seq using Self-Organizing Maps

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2023-12-01 | E-MTAB-13407 | biostudies-arrayexpress

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Project description:We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making. We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).

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Project description:Integrative single-cell RNA-seq and ATAC-seq analysis of mouse corneal epithelial cells

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2022-03-30 | GSE161600 | GEO

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