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One-pot universal NicE-seq: All enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

ABSTRACT: One-pot universal NicE-seq: All enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

PROVIDER: PRJNA733150 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14667234_1.fastq.gz	Fastqsanger.gz
	SRR14667234_2.fastq.gz	Fastqsanger.gz
	SRR14667235_1.fastq.gz	Fastqsanger.gz
	SRR14667235_2.fastq.gz	Fastqsanger.gz
	SRR14667236_1.fastq.gz	Fastqsanger.gz

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One-pot universal NicE-seq: All enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

Project description:Accessible chromatin landscape allows remodeling of transcription factors and enhancers during development and molecular subtypes of cancer in patient samples. One-tube universal NicE-seq (OuNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. OuNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in 25 fixed cells and opens the possibility for automation. Accessible chromatin profile is more efficient on formaldehyde fixed cells using OuNicE-seq compare to Tn5 transposon mediated methods, demonstrating its versatility.

2021-12-01 | GSE175651 | GEO

One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics.

Project description:BackgroundAccessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples.ResultsOne-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility.ConclusionOne-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn't require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation.

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Project description:Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen and FFPE tissue sections. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

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