Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Replication origin mapping in nda3-km311 and nda3-km311 rad3∆ in S. pombe

ABSTRACT: Identification of sites of replication initiation by copy number analysis, replicated DNA (time 80) vs unreplicated DNA (time 0).

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE98445 | GEO | 2018/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Replication origin mapping in cdc25-22 rif1∆ and cdc25-22 rif1∆rad3∆ in S. pombe

Project description:Identification of sites of replication initiation by copy number analysis, replicated DNA vs unreplicated DNA

2018-05-31 | GSE98446 | GEO

Replication origin mapping in cdc25-22 and cdc25-22 rad3∆ in S. pombe

Project description:Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase.

2018-05-31 | GSE98444 | GEO

Density Transfer Data for Lachancea waltii DNA Replication Profile

Project description:Array data detailing the progression of DNA replication in the yeast Lachancea waltii. L. waltii cells were pregrown in heavy isotope medium and synchronized at early S phase. They were then released into normal medium, wherein DNA replication proceeds. Replicated DNA molecules are thus of heavy-light (HL) composition as compared to unreplicated molecules, which are heavy-heavy (HH). 4 time points were taken and the percent of heavy-light DNA was determined at each time point. The heavy-heavy and heavy-light DNA molecules were separated by ultracentrifugation, differentially labeled, and hybridized to a genomic array for L. waltii. The array thus shows the progression of DNA replication.

2012-05-09 | E-GEOD-35155 | biostudies-arrayexpress

Single-cell DNA replication sequencing (scRepli-seq): a method for mapping replication timing domains genome wide in single mammalian cells

Project description:Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require a large number of S-phase cells for either effective enrichment of replicating DNA through BrdU immunoprecipitation or the determination of copy number differences during S-phase, which restricts their application to non-abundant cell types. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on the whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy number differences that arise between replicated and unreplicated DNA. We also provide computational pipelines that are key components of the methodology. NGS library preparation takes 3 d.

2020-10-07 | GSE138634 | GEO

ChIP-on-chip of RPA (Ssb1) in cdc25-22 and cdc25-22 rad3∆ in S. pombe

Project description:ChIP-on-chip of RPA at time 80' after cdc25-22 release

2018-05-31 | GSE98447 | GEO

Genome-wide stability of DNA replication program in single mammalian cells

Project description:We report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

2018-12-13 | GSE108556 | GEO

Genome-wide map of DNA replication origin in Schizosaccharomyces pombe

Project description:DNA replication origins, or DNA sites pre-RC is bound to, were identified by ChIP-seq of pre-RC components, Orc4 and Mcm2. DNA copy number analysis revealed that ~40% of the detected sites were efficient and early-firing origins.

2019-01-19 | GSE125335 | GEO

Yeast replication in the presence of MMS: WT and isw2 nhp10 strains

Project description:The eukaryotic DNA replication machinery must traverse every nucleosome present in the eukaryotic genome during S phase. Since nucleosomes are generally inhibitory to DNA-dependent processes, it is thought that chromatin structure must undergo extensive reorganization to facilitate DNA synthesis. However, the identity of chromatin-remodeling factors involved in replication and how they affect DNA synthesis is largely unknown. Here we show that two ATP-dependent chromatin-remodeling complexes in Saccharomyces cerevisiae, Isw2 and Ino80, function in parallel to promote DNA replication, especially during periods of replication stress. The rate of replication-fork progression is slowed when both chromatin-remodeling pathways are compromised. Both Isw2 and Ino80 complexes are recruited to actively replicating chromatin suggesting that these chromatin-remodeling complexes act directly to promote replication-fork progression. These findings support an important role for ATP-dependent chromatin-remodeling complexes in promoting DNA replication, and define specific stages of replication that require remodeling activity for normal function. A critical part of this study was the use of microarrays to measure DNA replication progression throughout the genome during MMS treatment. These samples are from experiments where we competed newly replicated DNA against unreplicated DNA on the same microarrays. Keywords: Time course

2007-11-30 | GSE9122 | GEO

The Schizosaccharomyces pombe rad3 checkpoint gene.

Project description: Not available

| S-EPMC452488 | biostudies-other

Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast

Project description:Ribosomal DNA (rDNA) is organized as large arrays of tandem repeats that vary in copy number from a few dozen to hundreds. In the budding yeast Saccharomyces cerevisiae, each rDNA repeat includes a potential origin of replication. Previous work has led to the model that the rDNA replication origins compete for limiting replication initiation factors with origins in the rest of the genome, suggesting that reduction in rDNA copy number would reduce competition for these limiting factors and therefore promote origin usage in the rest of the genome. To test this hypothesis, we compared genome-wide replication in strains with either wild type rDNA copy number of ~180 (“180 rDNA”) or just ~35 copies (“35 rDNA”) by performing dense-to-light isotope transfer experiments to physically separate replicated, hybrid-density (HL or heavy-light) DNA from unreplicated, HH (heavy-heavy) DNA in cell samples collected at different times in S phase. Contrary to our expectations, we find that although there are no apparent differences in non-rDNA origin activity between the two strains, the 35 rDNA strain shows a genome-wide delay in progression through S phase compared to the 180 rDNA strain.

2023-02-17 | GSE205068 | GEO

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