Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-MGH2-10-11-2015-05:01:11:768-248 - samples

ABSTRACT: Whole genome sequences of ACC primagrafts, Histone modification maps and transcription factor binding maps for ACC primagrafts and primary tumors. Processed ChIP-seq data is available on GEO under accession number GSE76465.

PROVIDER: EGAD00001001662 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

Drier Yotam Y Cotton Matthew J MJ Williamson Kaylyn E KE Gillespie Shawn M SM Ryan Russell J H RJ Kluk Michael J MJ Carey Christopher D CD Rodig Scott J SJ Sholl Lynette M LM Afrogheh Amir H AH Faquin William C WC Queimado Lurdes L Qi Jun J Wick Michael J MJ El-Naggar Adel K AK Bradner James E JE Moskaluk Christopher A CA Aster Jon C JC Knoechel Birgit B Bernstein Bradley E BE

Nature genetics 20160201 3

Translocation events are frequent in cancer and may create chimeric fusions or 'regulatory rearrangements' that drive oncogene overexpression. Here we identify super-enhancer translocations that drive overexpression of the oncogenic transcription factor MYB as a recurrent theme in adenoid cystic carcinoma (ACC). Whole-genome sequencing data and chromatin maps highlight distinct chromosomal rearrangements that juxtapose super-enhancers to the MYB locus. Chromosome conformation capture confirms th ...[more]

PMID: 26829750

Similar Datasets

Mapping of Polycomb binding in Drosophila larval brain tissue using DamID

Project description:We made Polycomb (PC) and histone H3 lysine 27 trimethylation (H3K27me3) chromatin binding maps in central brain tissue from 3rd instar larvae, allowing us to make a direct comparison to our 4C data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23166). Our results demonstrate that our PC and H3K27me3 maps are highly similar, and fit with previously identified hallmarks of PcG-bound chromatin, namely: PC and H3K27me3 co-occur in the genome as large contiguous domains that largely repress transcription of the underlying genes, which encode important regulators of development. Keywords: Genome binding/occupancy profiling by genome tiling array

2011-12-31 | GSE23298 | GEO

Mapping of H3K27me3 enrichment in Drosophila larval brain tissue using ChIP-chip

2011-12-31 | GSE23299 | GEO

High-throughput sequencing reveals a simple model of nucleosome energetics

Project description:We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on highthroughput nucleosome positioning maps are biased by experimental artifacts. Included are raw (eland) and mapped (wig) reads. The mapped reads are provided in eland and wiggle formats, and the raw reads are included in the eland file. This series includes only Mnase control data. The sonicated control is part of this already published accession, as is a in vitro nucleosome map: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15188 We also studied data (in vitro and in vivo maps as well as a model) from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13622 and from: http://www.ncbi.nlm.nih.gov/sra/?term=SRA001023

2010-08-20 | E-GEOD-23712 | biostudies-arrayexpress

Mapping of Polycomb binding in Drosophila larval brain tissue using DamID

2011-12-31 | E-GEOD-23298 | biostudies-arrayexpress

Mapping of H3K27me3 enrichment in Drosophila larval brain tissue using ChIP-chip

2011-12-31 | E-GEOD-23299 | biostudies-arrayexpress

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis

2016-03-15 | GSE76391 | GEO

TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana

Project description:This SuperSeries is composed of the SubSeries listed below. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199202 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199203

2022-03-23 | GSE199211 | GEO

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis

Project description:We recently developed a high-resolution genome wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) (GEO accession: GSE67941) We have now used this assay to assay the effect of chromatin state on DNA repair. Here we report the results of a time-course of the repair of the UV induced damages cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in normal human skin fibroblasts. Comparison of this data to histone modification and DNA-seq maps (ENCODE) revealed initial repair of both damages is enriched in open and active chromatin states, whereas repair in heterochromatic and repressed chromatin states is relatively low and persists to later time points. We performed XR-seq for two types of UV induced damages (CPD and (6-4)PP) at multiple time points after UV irradiation, in normal NHF1, and CS-B (CS1ANps3g2, GM16095) fibroblast cell lines. Two biological replicates were performed for each experiment in which independent independent cell populations were UV treated and subjected to XR-seq. For assaying CPD repair, cells were irradiated with 10J/m2 and for assaying (6-4)PP cells were irradiated with 20J/m2. Raw data for the 1h time points of (6-4)PP repair are the same as in GEO accession GSE67941).

2016-03-15 | E-GEOD-76391 | biostudies-arrayexpress

Role of SMARCAD1 and H3R26Cit in Maintenance of the Naïve Pluripotent State

Project description:Genome-wide maps of SMARCAD1 binding and histone modification H3R26Cit in mouse ES cells, histone modification H3K9me3, H3K4me3, H3K27Ac in Smarcad1 KD mouse ES cells, and histone modification H3K9me3 in mouse ES cells after PADI inhibition. Together with RNA-seq data for mouse ICM, blastocyst, embryonic stem cells and Smarcad1 KD cells.

2017-04-10 | GSE45338 | GEO

RNA-seq of coding RNA from mouse tissues harvested from 8-week old male C57BL/6 mice (ENCODE/UW)

Project description:This experiment is contains a subset of mouse organism part samples and RNA-seq data from experiment E-GEOD-39524 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39524/), which was originally submitted by the ENCODE consortium to NCBI Gene Expression Omnibus under accession number GSE39524 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE39524) and later imported to ArrayExpress as E-GEOD-39524.

2012-07-20 | E-MTAB-2685 | 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