Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Maize earshoot MOA-seq open chromatin profiling using micrococcal nuclease with formaldehyde-crosslinked nuclei.

PROVIDER: PRJNA477338 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10747872_1.fastq.gz	Fastqsanger.gz
	SRR10747872_2.fastq.gz	Fastqsanger.gz
	SRR10747873_1.fastq.gz	Fastqsanger.gz
	SRR10747873_2.fastq.gz	Fastqsanger.gz
	SRR10747874_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 41

Similar Datasets

Genomewide profiling of differentially H3K4me3 marked genes in colon cancer cells versus normal colon epithelial cells.

Project description:To identify differentially marked genes with a narrow or broad H3K4me3 pattern, we performed ChIP-seq using formaldehyde crosslinked chromatin from three colorectal cancer cell lines and normal colonic epithelial cell line and was digested with micrococcal nuclease to the extent that 70% of the chromatin was cleaved to mononucleosomes.

2025-04-02 | GSE286296 | GEO

Genome-wide mapping of open chromatin in mouse embryonic stem cell

Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected.

2013-10-01 | GSE50706 | GEO

Genome-wide mapping of open chromatin in mouse embryonic stem cell

2013-10-01 | E-GEOD-50706 | biostudies-arrayexpress

Mapping of mononucleosomal DNA in wild type Drosophila

Project description:Crosslinked chromatin from wild-type flies was digested with micrococcal nuclease. Mononucleosomal DNA was gel-purified and hybridized to Affymetrix tiling arrays.

2008-05-20 | E-MEXP-1519 | biostudies-arrayexpress

HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

Project description:Analysis of histone H3 turnover in wild-type and mutant fission yeast cells by using MNase-ChIP-chip Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose. Cells were crosslinked with 1% Formaldehyde and chromatin was fragmented into mononucleosomes by using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody from wild-type and mutant fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto 44k pombe Agilent oligo arrays. Data were processed using Agilent scanner and Feature Extraction software.

2013-04-21 | E-GEOD-45378 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila DNA to identify nucleosomes bound by RNA polymerase II

Project description:Crosslinked chromatin was digested with Micrococcal nuclease and immunopurified for Rpb3, a subunit of RNA Polyermase II. chIP'd DNA was hybridized to Drosophila tiling arrays and nucleosomes that were bound by Pol II were mapped.

2008-05-20 | E-MEXP-1515 | biostudies-arrayexpress

In vivo nucleosome occupancy in yeast (MNase-seq)

Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast. Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion

2013-01-06 | E-GEOD-34923 | biostudies-arrayexpress

DNA sequence at CpG islands directly influences chromatin structure via the CpG binding protein Cfp1

Project description:CpG islands (CGIs) are prominent in the mammalian genome due to their G+C rich base composition and high density of CpG dinucleotides. Most mammalian gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3),irrespective of transcriptional activity. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. High throughput sequencing of Cfp1-bound chromatin identified a striking concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Protocol: Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication (Skene et al, Mol Cell, 2010). Cells were crosslinked using 1% formaldehyde and chromatin sheared using sonication.Protein-DNA complexes were immunoprecipitated with the appropriate antibody and DNA was subsequently extracted. Adaptors were ligated to purified DNA which was then amplified by PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2012-07-18 | E-ERAD-79 | biostudies-arrayexpress

Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.

Project description:Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle. We determined genes preferentially expressed in muscle cells of adult C. elegans by analyzing RNA from total and affinity-puridied muscle nuclei using microarrays. We also determined the nucleosome occupancy in these nuclei by micrococcal nuclease mapping and paired-end sequencing.

2011-12-05 | E-GEOD-31602 | biostudies-arrayexpress

MPE-seq, a New Method for the Genome-wide Analysis of Chromatin Structure

Project description:In this study we developed MPE-seq, a method for the genome-wide characterization of chromatin that involves the digestion of nuclei with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. We also performed MNase-seq as a comparison. We further performed ChIP-seq using chromatin samples obtained by MPE-Fe(II) or MNase digestion of nuclei.

2015-06-16 | GSE69098 | 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