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CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

ABSTRACT: CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

PROVIDER: PRJNA856663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20020482_1.fastq.gz	Fastqsanger.gz
	SRR20020482_2.fastq.gz	Fastqsanger.gz
	SRR20020483_1.fastq.gz	Fastqsanger.gz
	SRR20020483_2.fastq.gz	Fastqsanger.gz
	SRR20020484_1.fastq.gz	Fastqsanger.gz

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scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

2024-09-06 | GSE249799 | GEO

CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

Project description:We report the application of CUT&Tag sequencing technology for high-throughput profiling of c-Myc with core promoters of its target genes in mammalian cells. We performed CUT&Tag sequencing with antibody to total c-Myc with core promoters of its target genes in CTRLcas9 and SCARB2cas9 group. Inspection of multiple individual traces and global analyses showed that SCARB2cas9 globally reduced association of c-Myc with core promoters of its target genes.

2023-08-11 | GSE207672 | GEO

Genome-wide Maps of Chromatin State in Control and DEK-deficient Hematopoietic Stem Cells [CUT&Tag]

Project description:Purpose:To identify chromatin state involved in the DEK regulating gene expression of hematopoietic stem cells (HSC) in mice, we performed DEK, H3K27ac, H3K4me3 and H3K9ac CUT&Tag in HSC or LSK cells freshly sorted from mice.

2021-02-22 | GSE166433 | GEO

Genome-wide maps of chromatin state in HepG2 cells.

Project description:Genome-wide maps of chromatin state in HepG2 cells.

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Genome-wide maps of chromatin state in HepG2 cells

Project description:Genome-wide maps of chromatin state in HepG2 cells

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CUT&Tag profiling of HNF4A in HT29 cell lines after the depletion of PINK1

Project description:The experiment contains CUT&Tag profiles for transcription factor HNF4A in HT29 cell line treated with shRNA for PINK1. The experiment also include a control profile for HNF4A in HepG2 cell line.

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Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

2022-02-15 | GSE178559 | GEO

Genome-wide Maps of Chromatin State in Control and DEK-deficient Hematopoietic Stem Cells [CUT&Tag]

Project description:Genome-wide Maps of Chromatin State in Control and DEK-deficient Hematopoietic Stem Cells [CUT&Tag]

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Project description:We recently introduced CUT&Tag, an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei, and then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds DNA sequencing adapters (“tagmentation”) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses exposure artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves signal-to-noise over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube from cells to amplified libraries, providing low-cost high-resolution genome-wide chromatin maps. By simplifying library preparation, CUT&Tag requires less than a day at the bench from live cells to sequencing-ready barcoded libraries. Because of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for ~$25 per sample, enabling routine genome-wide profiling of chromatin proteins and modifications that requires no special skills or equipment.

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Project description:HCT116_SMARCA4 CUT&Tag

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