Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA700961 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

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

Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

| PRJNA686390 | ENA

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

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

Structural basis of the DEK-nucleosome complex and its functional implications (CUT&Tag)

Project description:The nuclear factor Dek is notably enriched within chromatin; nevertheless, the precise binding mechanism of Dek to the nucleosome remains elusive. In this study, we employ cryo-electron microscopy (cryo-EM) to elucidate the high-resolution structure of the Dek-Nucleosome Core Particle (NCP) complex. We identify specific domains responsible for DEK interaction with the histone octamer and DNA within the nucleosome. The veracity of these binding domains is confirmed through a series of meticulous biochemical experiments. Subsequently, cellular experiments reveal that Dek lacking nucleosome-binding capacity exhibits a deficiency in chromatin interaction. Remarkably, this impairment induces a shift towards the primitive endoderm fate in mouse embryonic stem cells, underscoring the pivotal role of Dek in determining cell fate through its nucleosomal interactions.

2024-01-15 | GSE253062 | 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

CUT&TAG of OE19 cell line

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

CUT-tag analysis of C1qbp sufficient and deficient CD8+ T cells

Project description:This study is aimed to Investigate whether C1qbp deficiency affects the histone modification during the differentiation stage of CD8+ T cells. Transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong were collected and treated for CUT-tag. CUT-tag-Seq analysis provided evidence of histone modification changes between WT and C1qbp KO CD8+ T cells. Our study shows that on day 5 post-infection with LCMV Armstrong, along with mRNA expressing profiling, the CUT-tag-seq exhibits obvious changes in H3K27me3 and H3K27Ac modification of indicated genes of WT and C1qbp KO CD8+ T cells.

2021-06-09 | GSE176368 | GEO

Genome-wide maps of histone lactylation in ocular melanoma by CUT&Tag

Project description:To investigate the function of histone lactylation in ocular melanoma, we analyzed histone lactylation enrichment level in ocular melanoma by CUT&Tag.

2023-09-04 | GSE242018 | GEO

The proto-oncogene DEK regulates neuronal excitability and tau accumulation in Alzheimer’s disease vulnerable neurons [chromatin]

Project description:Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. We used a data-driven functional genomics approach to model ECII neurons in silico that led us to the prediction that the proto-oncogene DEK is a driver of tau pathology in these neurons. In order to understand the function of DEK in vulnerable neurons, we modulated its expression in ECII neurons in vitro and in vivo in the mouse. Since DEK is a chromatin modulator, we investigated the genomic location of a few histone marks in DEK silenced cells using the CUT&TAG approach, as well as Chromatin Accessibility using ATAC-seq

2022-05-22 | GSE203364 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data