Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms

ABSTRACT: We report the development of a versatile strategy to map nucleosomes in multiple model organisms

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe Neurospora crassa

PROVIDER: GSE141676 | GEO | 2019/12/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms.

Project description:MNase-seq (micrococcal nuclease sequencing) is used to map nucleosome positions in eukaryotic genomes to study the relationship between chromatin structure and DNA-dependent processes. Current protocols require at least two days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for S. cerevisiae and other fungi which takes only three hours. Modified protocols were developed for wild fungi and mammalian cells. This method for rapidly producing sequencing-ready nucleosome footprints from several organisms makes MNase-seq faster and easier, with less chemical waste.

| S-EPMC8141940 | biostudies-literature

Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms

Project description:Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms

| PRJNA594357 | ENA

organisms

Project description:organisms Raw sequence reads

| PRJNA825711 | ENA

Soil organisms

Project description:Soil organisms Targeted loci environmental

| PRJNA1088460 | ENA

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

Project description:Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that are activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead there was an increase in the accessibility of nucleosomes, as measured by MNase digestion and by ATAC-seq, that did not result from removal of the nucleosome. Thus changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.

2017-06-06 | GSE95689 | GEO

cellular organisms

Project description:Genome sequencing of microbial organisms in Japan Collection of Microorganisms

| PRJDB20694 | ENA

cellular organisms

Project description:Genome sequencing of microbial organisms in Japan Collection of Microorganisms

| PRJDB20344 | ENA

cellular organisms

Project description:Genome sequencing of microbial organisms in Japan Collection of Microorganisms

| PRJDB20346 | ENA

cellular organisms

Project description:Genome sequencing of microbial organisms in Japan Collection of Microorganisms

| PRJDB20693 | ENA

High resolution maps of nucleosome position and interactions

Project description:Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method – termed Proximity Copy Paste (PCP) – we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays. The properties of the arrays differs according to transcriptional activity with short delocalized arrays dominating the most highly transcribed genes. Additionally, by mapping long-range, multi-way interactions we provide evidence for the longstanding hypothesis that metaphase chromosomes are compacted by arrayed cohesin hubs. Using single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that noncanonical nucleosomes are a stable feature of chromatin. PCP is a versatile method allowing the connectivity of individual molecules to be mapped at high-resolution

2025-06-12 | GSE275421 | 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