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ABSTRACT: CUT&Tag applicable to help find biologically meaningful SNP

PROVIDER: PRJNA898148 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR22188620_1.fastq.gz	Fastqsanger.gz
	SRR22188620_2.fastq.gz	Fastqsanger.gz
	SRR22188621_1.fastq.gz	Fastqsanger.gz
	SRR22188621_2.fastq.gz	Fastqsanger.gz
	SRR22188622_1.fastq.gz	Fastqsanger.gz

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To find target genes of Zeb1 [CUT&Tag-Seq]

Project description:To find target genes of Zeb1 [CUT&Tag-Seq]

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Comparative analyses of ChIP-seq, CUT&RUN and CUT&Tag for Polycomb chromatin profiling

Project description:Chromatin profiling methods such as ChIP-seq, CUT&RUN, and CUT&Tag differ substantially in background structure, signal distribution, and resolution, complicating direct quantitative comparison across platforms. In this study, we systematically compared conventional and double-crosslink ChIP-seq, CUT&RUN, and CUT&Tag by profiling the Polycomb-associated histone modification H3K27me3 in human cardiomyocytes and the PRC2 catalytic subunit EZH2 in pluripotent stem cells. To enable cross-assay comparison, we developed a biologically informed normalization strategy based on stable Polycomb reference loci, allowing harmonization of signal scales while preserving assay-intrinsic signal architecture. This approach revealed that CUT&RUN preferentially captures broad H3K27me3 domains, whereas CUT&Tag provides sharper and more localized enrichment for both H3K27me3 and EZH2. Together, our results establish a practical framework for cross-platform epigenomic comparison and guide the selection of chromatin profiling strategies. This GEO submission includes only datasets newly generated in this study. Additional publicly available datasets analyzed for comparison are cited in the associated manuscript and were not re-submitted here.

2026-05-12 | GSE314247 | GEO

Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis II

Project description:Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K27ac, H3K9me3, H3K4me3, and H3K36me3 in mESCs cells.

2026-07-16 | GSE324892 | GEO

CUT&Tag for DUX recruitment,domain-influenced chormatin modifications, and a potential binding partner with a member of the SWI/SNF complex

Project description:In order to determine that CUT&Tag is similar to known DUX ChIP-seq, we performed CUT&Tag with a mCherry-tagged DUX (with the mCherry antibody). Once confirmed, we pewrformed CUT&Tag for other DUX derivatives with their mCherry tag Then, we performed CUT&Tag for H3K9ac, which is known to globally increase in 2-cell-like cells, which occurs after DUX expression, and CUT&Tag for SMARCC1, a subunit of the SWI/SNF complex

2023-08-07 | GSE224297 | GEO

Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis [Crosslinking]

Project description:Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K7me3 in mESCs and rat C6 cells. For CTCF 50K cells are needed. EGS crosslinking and de-duplication strategies were also explored.

2026-07-16 | GSE310696 | GEO

Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis [Cell number]

Project description:Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K7me3 in mESCs and rat C6 cells. For CTCF 50K cells are needed. EGS crosslinking and de-duplication strategies were also explored.

2026-07-16 | GSE310695 | GEO

Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis

Project description:Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K7me3 in mESCs and rat C6 cells. For CTCF 50K cells are needed. EGS crosslinking and de-duplication strategies were also explored.

2026-07-16 | GSE311434 | GEO

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

A protocol for high-throughput microplate-based CUT&Tag

Project description:Cleavage Under Targets & Tagmentation (CUT&Tag) is a versatile method for measuring genomic occupancy of chromatin-associated proteins with high sensitivity and specificity. CUT&Tag has low sequencing requirements and is therefore suitable for highly multiplexed experiments, but methods to process samples at throughput without specialized equipment are lacking. Here we present a method for simultaneous parallel processing of 96 CUT&Tag samples in a standard microplate. Plate-CUT&Tag can be carried out in a similar time frame to benchtop CUT&Tag and yields data of comparable quality. We present data from cell culture and patient leukemia samples processed with Plate-CUT&Tag to illustrate its utility in large-scale preclinical and translational studies.

2025-09-18 | GSE308505 | GEO

CUT&Tag and BioCUT&Tag enables investigation of the AT-rich epigenome of Plasmodium falciparum from low input samples

Project description:This study aimed to adapt CUT&Tag to Plasmodium falciparum samples as an efficient and sensitive alternative to classical ChIP-sequencing. We compare H3K9me3 and HP1 CUT&Tag with ChIP-seq datasets, showing successful establishment of CUT&Tag in P. falciparum. Next we aimed to scale down required input material for our CUT&Tag reactions and generated high-quality HP1 tracks with as little as 10.000 nuclei. To minimise potential sample loss we tested feasibility of utilising (frozen) saponin parasite isolates as input material instead of nuclei, which proved to be viable. Lastly, we deployed our new technique Dimerisation-induced Biotinylation-CUT&Tag (DiBioCUT&Tag) to catch transient interactions by biotinylation of strongly associated proteins such as histones. We tested this technique on HP1 and compared standart CUT&Tag with DiBioCUT&Tag. Furthermore, we explored interactions of the transcription factor BDP5, which we were previously unable to succesfully ChIP.

2024-06-27 | GSE270104 | GEO

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