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 HepG2 cells

ABSTRACT: We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in HepG2 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE184796 | GEO | 2022/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide maps of chromatin state in Huh 7 cells

Project description:We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in Huh 7 cells.

2022-03-01 | GSE184797 | GEO

Genome-wide maps of chromatin state in HepG2 cells.

Project description:Twist1 related genes detected by chipseq

2021-06-30 | GSE133376 | GEO

Genome-wide maps of chromatin state in saccharomyces cerevisiae

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in yeast. By obtaining bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of saccharomuces cerevisiae.We find that H3T11 phosphorylationlysine is widely distributed in gene promoter region and chromosome telomere region

2020-03-12 | GSE146821 | GEO

ATAC-seq of HepG2 cells

Project description:ATAC-seq open chromatin maps for HepG2 cells (3 biological replicates), a liver model.

2019-03-20 | E-MTAB-7543 | biostudies-arrayexpress

Genome-wide maps of chromatin state in human monocytes and monocyte-derived DCs

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in human monocyte devried DCs. By obtaining about 15 million mapped reads for each sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human monocytes and monocyte-derived DCs. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

2016-11-19 | GSE52510 | GEO

Genome-wide maps of chromatin state in neural stem/progenitor cells (NSC) from mouse neonatal forebrain [ChIP-seq]

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in NSC. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of NSC. We compared histone modifications between wild type and Sox2-deleted NSC.

2019-03-07 | GSE90558 | GEO

Genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells.

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of c-Myc with core promoters of its target genes in mammalian cells. We performed ChIP 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 | GSE185838 | GEO

ATAC-seq of HepG2 cells

Project description:ATAC-seq of HepG2 cells

| PRJEB30461 | ENA

Genome-wide maps of HNF4a and HNF4g binding state in HepG2 cells.

Project description:Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady state remains to be elucidated. Here we report the native HNF4α isoforms, phosphorylation status and complexes in the steady state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semi-quantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and Hepatocyte nuclear factor-4γ was found. A biochemical and genome-wide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here is important for an accurate understanding of transcriptional regulation. Examination of HNF4alpha binding sites with domain-specific antibodies and HNF4gamma binding sites in HepG2 cell.

2010-12-22 | E-GEOD-18989 | biostudies-arrayexpress

Genome-wide maps of chromatin state in liver cells.

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse liver cells. We find that lysine 4 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 9 and 27 trimethylation marks primary coding and non-coding transcripts, have no differents in gene annotation. Trimethylation of lysine 4 is detected has different expresssion at mir124 site front of lnc-RNA(10835)Far. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

2020-03-08 | GSE128073 | GEO

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