Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq of C3H mouse livers

ABSTRACT: This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse livers with such processes as replication, transcription, and interaction of DNA with proteins. Liver samples of 15-day old (P15) untreated C3H/HeOuJ mice were isolated and flash-frozen. ATAC-seq was performed to identify the regions of open chromatin and sites likely to be occupied by transcription factors.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Duncan Odom

PROVIDER: E-MTAB-11780 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq of Fh1-WT, Fh1-KO and Fh1-rec cells

Project description:To identify accessible regions of the genome, we performed ATAC-seq.

2022-09-01 | E-MTAB-11789 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma WTSI-OESO_009 (CAM408) organoid treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on WTSI-OESO_009 cells treated with 1000 nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10306 | biostudies-arrayexpress

ATAC-seq of OE19 cells treated with either siNT or siERBB2

Project description:To investigate the effect on chromatin accessibility with reduced ERBB2 signalling in oesophageal adenocarcinoma, we performed ATAC-seq in OE19 cells treated with either siNT or siERBB2.

2020-09-30 | E-MTAB-8576 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma KYAE1 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on KYAE1 cells treated with 500 nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10310 | biostudies-arrayexpress

ATAC-seq of human gastric adenocarcinoma NCI-N87 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on NCI-N87 cells treated with 250nM lapatinib for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10313 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib

Project description:To investigate changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on OE19 cells treated with 500 nM lapatinib for 1, 7 and 35 days and vehicle control (DMSO) for 1 day.

2022-09-26 | E-MTAB-10302 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma ESO26 cell line treated with lapatinib

Project description:To investigate initial changes to chromatin accessibility associated with resistance to lapatinib, we performed ATAC-seq on ESO26 cells treated with 500 nM lapatinib plus 1000 nM MK-2206 (an AKT inhibitor) for 24 hours and vehicle control (DMSO) for 24 hours.

2022-09-26 | E-MTAB-10307 | biostudies-arrayexpress

ATAC-seq of oesophageal adenocarcinoma patient samples

Project description:Open chromatin profiling (ATAC-seq) of human oesophageal adenocarcinoma patient samples.

2020-09-30 | E-MTAB-8447 | biostudies-arrayexpress

ATAC-seq of human oesophageal adenocarcinoma OE19 cell line treated with lapatinib for 35 days followed by drug withdrawal

Project description:To investigate whether changes to chromatin accessibility associated with resistance to lapatinib are a stable or a reversible state, we treated OE19 cells with 500 nM lapatinib for 35 days and then withdrew lapatinib for 1, 2, 3 and 14 days. Control cells treated with DMSO for 1 day and 'resistant' cells treated with 500 nM lapatinib for 35 days were also sequenced.

2022-09-26 | E-MTAB-10314 | biostudies-arrayexpress

HNF4A is required to specify glucocorticoid action in the liver - ATACseq

Project description:The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR are highly dependent on cell type and environmental context. Here, we demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver-specificity of GR action. In normal mouse liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites leads to loss of GR binding at weak GRE motifs. GR binding is gained at sites characterised by strong GRE motifs, which typically show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is further demonstrated by evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.

2022-01-20 | E-MTAB-10266 | biostudies-arrayexpress

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