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ABSTRACT: H3K9ac CUT&Tag sequencing for silkworms

PROVIDER: PRJNA1098611 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28607936_1.fastq.gz	Fastqsanger.gz
	SRR28607936_2.fastq.gz	Fastqsanger.gz
	SRR28607937_1.fastq.gz	Fastqsanger.gz
	SRR28607937_2.fastq.gz	Fastqsanger.gz
	SRR28607938_1.fastq.gz	Fastqsanger.gz

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Chromatin landscape of H3K9ac and its modifier GCN5 in the malaria parasite

Project description:This study is to analyze the chromatin landscape of the active mark H3K9ac, an active mark catalyzed by GCN5, and GCN5 in the malaria parasite Plasmodium falciparum at the schizont stage by both ChIP-seq and CUT&Tag-seq for H3K9ac and CUT&Tag-seq for GCN5.

2025-06-09 | GSE284527 | 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

Study the role of different concentrations of VFAs on histone modifications in ovine ruminal epithelial cells at am and pm using CUT&Tag-seq

Project description:This experiment employed CUT&Tag-seq (Cleavage Under Targets and Tagmentation with sequencing) to explore the mechanism of how different concentrations of VFAs regulate ruminal epithelial histone modifications under the Grain-diet and Hay-diet patterns in both am and pm. Cells from Grain-am, Grain-pm, Hay-am, and Hay-pm treatment groups were havest for CUT&Tag-seq experiments, n=3 pooled biological replicates per library. The primary histones used for CUT&Tag were Acetyl-Histone H3 (Lys27) Rabbit mAb (H3K27ac, 8173S, CST), Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb (H3K9ac, 9649S, CST), and Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb (H3K4me3, 9751S, CST).

2025-01-08 | GSE286161 | GEO

H3K9ac and H3K27ac Cut&Tag profiling of wild type and Rbm25-deficient Bone Marrow Derived macrophage

Project description:Purpose: To transcriptome widely reveal histone acetylation modification H3K9ac and H3K27ac regulation by Rbm25, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) and Rbm25-deficiency BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25 deficient BMDMs were stimulated with LPS (100ng/ml) for 4 hours. Results: We carried out CUT&Tag assays using antibody against H3K9ac or H3K27ac, and found the global influence of Rbm25 in regulating H3K9ac and H3K27ac of transcription regulatory regions of key genes for inflammatory macrophage effector function.

2024-11-06 | GSE240158 | GEO

histone H3K9 acetylation for syncytialization of human placental trophoblast stem cells

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2024-08-02 | GSE246277 | 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

Epigenetic effects (H3K9ac, H3K14ac, H3K23ac and Pol II) of Kat6b loss in mouse neural stem cells (CUT&Tag)

Project description:Heterozygous mutations in the histone acetyltransferase gene KAT6B (MYST4/MORF/QKF) cause cognitive disorders. Congruently, KAT6B is required for brain development, neural stem cell self-renewal and neuronal differentiation in mice. Despite the clear requirement for KAT6B in brain development, its molecular roles remain unexplored. Here we use CUT&Tag sequencing to determine the effects of loss or gain of KAT6B on H3K9ac and H3K23ac histone marks and on RNA Pol II.

2024-11-06 | GSE267672 | 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

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

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