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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE311434 | GEO | 2026/07/16

REPOSITORIES: GEO

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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]

2026-07-16 | GSE310695 | 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

Low-cost high-resolution chromatin profiling with CUT&Tag

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.

2020-07-15 | GSE145187 | GEO

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

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

| PRJNA1369458 | ENA

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

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

| PRJNA1438065 | ENA

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

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

| PRJNA1366956 | ENA

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

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

| PRJNA1366954 | ENA

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

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

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