Cut&Tag-sequencing
Ontology highlight
ABSTRACT:
TISSUE(S): ['stem Cell']
SUBMITTER: Dacheng Jiang
PROVIDER: OEX00029067 | NODE | 2024-10-25
REPOSITORIES: NODE
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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
Project description:To map the chromatin binding sites for SMC1 in OE19 cells, we performed CUT&TAG.
2024-09-25 | E-MTAB-14090 | biostudies-arrayexpress
Project description:We performed the cleavage under targets and tagmentation (Cut & tag) assay followed by sequencing enriched DNA fragments to reveal the direct downstream targets of Pbx1. Firstly, we overexpressed Pbx1b with Pbx1b-IRES-GFP retrovirus in murine peripheral B cells to ensure the yields of DNA fragments. CUT & tag libraries were generated following instructions of the manufacturer’s protocol (Vazyme; cat TD901-01) and the Pbx1 antibody (CST; cat 4342) was used for signal enrichment.
2023-03-26 | E-MTAB-12769 | biostudies-arrayexpress
Project description:Precise profiling of epigenomes, including histone modifications and transcription factor binding sites, is essential for better understanding gene regulatory mechanisms. Cleavage Under Targets & Tagmentation (CUT&Tag) is an easy and low-cost epigenomic profiling method that can be performed on a low number of cells and at the single-cell level. A large number of CUT&Tag datasets have been generated in various biological systems, providing a valuable resource. CUT&Tag experiments use the hyperactive transposase Tn5 for tagmentation. We found that the preference of Tn5 captured reads toward accessible chromatin regions can influence the distribution of CUT&Tag reads and cause open chromatin biases, further confounding the analysis of CUT&Tag data. The high sparsity of single-cell sequencing data makes the open chromatin biases more substantial than in bulk sequencing data. Here, we present a comprehensive computational method, PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), to mitigate the open chromatin bias inherent in CUT&Tag data at both bulk and single-cell levels. By integrating existing transcriptome and epigenome data using machine learning and comprehensive modeling, we demonstrate that PATTY yields more accurate and robust detection of occupancy sites for both active and repressive histone marks than existing methods, with experimental validation. We further designed a single-cell CUT&Tag analysis framework by utilizing this model and showing improved cell clustering from bias-corrected single-cell CUT&Tag data compared to using raw data. This model paved the way for further development of computational tools for improving bulk and single-cell CUT&Tag data analysis.
2026-02-06 | GSE298565 | GEO
Project description:CUT&Tag was performed to identify the effect of DIS3 depletion on DNA:RNA hybrids genome-wide. DIS3-AID HCT116 cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control). CUT&Tag was performed targeting DNA:RNA hybrids using the CUT&Tag-IT® R-loop Assay Kit (Active Motive) with the S9.6 antibody.
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Project description:To investigate the transcriptional regulation of Xbp1s in ILC2s, sorted large intestinal ILC2s from mice were used for CUT&Tag sequencing to analyze the target of Xbp1s.
2024-05-28 | GSE268234 | GEO
Project description:To investigate GLI3 TF targets during organoid fate decisions, we performed Cut&Tag of GLI3 binding
2022-08-28 | E-MTAB-12006 | biostudies-arrayexpress
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
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
Project description:To map the chromatin binding sites for various factors in OE19 cells, we performed CUT&TAG.
2023-02-24 | E-MTAB-11356 | biostudies-arrayexpress