Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chem-map: Profiling drug binding to chromatin in cells

ABSTRACT: Chem-map: Profiling drug binding to chromatin in cells

PROVIDER: PRJNA862136 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20652900_1.fastq.gz	Fastqsanger.gz
	SRR20652900_2.fastq.gz	Fastqsanger.gz
	SRR20652901_1.fastq.gz	Fastqsanger.gz
	SRR20652901_2.fastq.gz	Fastqsanger.gz
	SRR20652902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 288

Similar Datasets

Chem-map profiles drug binding to chromatin in cells.

Project description:Characterizing drug-target engagement is essential to understand how small molecules influence cellular functions. Here we present Chem-map for in situ mapping of small molecules that interact with DNA or chromatin-associated proteins, utilizing small-molecule-directed transposase Tn5 tagmentation. We demonstrate Chem-map for three distinct drug-binding modalities as follows: molecules that target a chromatin protein, a DNA secondary structure or that intercalate in DNA. We map the BET bromodomain protein-binding inhibitor JQ1 and provide interaction maps for DNA G-quadruplex structure-binding molecules PDS and PhenDC3. Moreover, we determine the binding sites of the widely used anticancer drug doxorubicin in human leukemia cells; using the Chem-map of doxorubicin in cells exposed to the histone deacetylase inhibitor tucidinostat reveals the potential clinical advantages of this combination therapy. In situ mapping with Chem-map of small-molecule interactions with DNA and chromatin proteins provides insights that will enhance understanding of genome and chromatin function and therapeutic interventions.

| S-EPMC10497411 | biostudies-literature

Chem-map: Profiling drug binding to chromatin in cells

Project description:We present a method of mapping binding sites of small molecules on chromatine targets in situ, in U2OS and K562 cell lines

2022-12-06 | GSE209713 | GEO

Chem-Seq of chemical derivatives in MM1S cells

Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome. We developed in vivo and in vitro Chem-Seq protocols with a biotinylated derivative of small molecules. In the in vivo protocol, Cells were first treated with biotinylated ligand and cross-linked with formaldehyde at the same time. Cells were then lysed, sonicated to shear the DNA, and streptavidin beads were used to isolate biotinylated ligand and associated chromatin fragments. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome. In in vitrol protocol, MM1.S cells were fixed and the derived sonicated lysate incubated with biotinylated drug to enrich for bound chromatin regions in vitro. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome.

2013-05-31 | E-GEOD-44098 | biostudies-arrayexpress

Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells (Chem-Seq)

Project description:We used Chem-seq to map the genome-wide distribution of the binding sequence of SAHA-PIP G.

2020-01-03 | GSE142859 | GEO

Chem-Seq of chemical derivatives in MM1S cells

2013-12-13 | GSE44098 | GEO

PM01183 on SCLC cell lines Chem-seq

Project description:Chem seq to compare the binding activity of biotynilated drugs.Lurbinectedin and cisplatin comparison

2022-01-29 | GSE190398 | GEO

A prostate cancer chromatin interaction map

Project description:A prostate cancer chromatin interaction map

| PRJNA486278 | ENA

A Comprehensive Binding and Functional Map of Human RNA-binding Proteins

Project description:A Comprehensive Binding and Functional Map of Human RNA-binding Proteins

| PRJNA866647 | ENA

PM01183 on SCLC cell lines Chem-seq

Project description:PM01183 on SCLC cell lines Chem-seq

| PRJNA786933 | ENA

Chromatin transaction map during vertebrate mitotic entry

Project description:We have used a combination of chemical genetics, chromatin proteomics and imaging to map the earliest chromatin transactions during vertebrate cell entry into mitosis. Chicken DT40 Cdk1as cells undergo synchronous mitotic entry within 15 minutes following release from a 1NM-PP1-induced arrest in late G2. In addition to changes in chromatin association with nuclear pores and the nuclear envelope, earliest prophase is dominated by changes in the association of ribonucleoproteins with chromatin, particularly in the nucleolus, where pre-rRNA processing factors leave chromatin significantly before RNA polymerase I. Nuclear envelope barrier function is lost early in prophase and cytoplasmic proteins begin to accumulate on the chromatin. As a result, outer kinetochore assembly appears complete by nuclear envelope breakdown (NEBD). Most interphase chromatin proteins remain associated with chromatin until NEBD, after which their levels drop sharply.

2022-01-31 | PXD026385 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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